diff --git a/.github/deployment/node/Dockerfile b/.github/deployment/node/Dockerfile
index 873d62daf..353642f9a 100644
--- a/.github/deployment/node/Dockerfile
+++ b/.github/deployment/node/Dockerfile
@@ -10,4 +10,4 @@ RUN apt-get update && \
   apt-get install -y --no-install-recommends openssl && \
   rm -rf /var/lib/apt/lists/*
 
-CMD ["node", "--import", "./scripts/register.js", "./dist/index.js"]
+CMD ["node", "./dist/main.js"]
diff --git a/.github/deployment/self-host/compose.yaml b/.github/deployment/self-host/compose.yaml
deleted file mode 100644
index dde7dc8ba..000000000
--- a/.github/deployment/self-host/compose.yaml
+++ /dev/null
@@ -1,60 +0,0 @@
-services:
-  affine:
-    image: ghcr.io/toeverything/affine-graphql:stable
-    container_name: affine_selfhosted
-    command:
-      ['sh', '-c', 'node ./scripts/self-host-predeploy && node ./dist/index.js']
-    ports:
-      - '3010:3010'
-      - '5555:5555'
-    depends_on:
-      redis:
-        condition: service_healthy
-      postgres:
-        condition: service_healthy
-    volumes:
-      # custom configurations
-      - ~/.affine/self-host/config:/root/.affine/config
-      # blob storage
-      - ~/.affine/self-host/storage:/root/.affine/storage
-    logging:
-      driver: 'json-file'
-      options:
-        max-size: '1000m'
-    restart: unless-stopped
-    environment:
-      - NODE_OPTIONS="--import=./scripts/register.js"
-      - AFFINE_CONFIG_PATH=/root/.affine/config
-      - REDIS_SERVER_HOST=redis
-      - DATABASE_URL=postgres://affine:affine@postgres:5432/affine
-      - NODE_ENV=production
-      # Telemetry allows us to collect data on how you use the affine. This data will helps us improve the app and provide better features.
-      # Uncomment next line if you wish to quit telemetry.
-      # - TELEMETRY_ENABLE=false
-  redis:
-    image: redis
-    container_name: affine_redis
-    restart: unless-stopped
-    volumes:
-      - ~/.affine/self-host/redis:/data
-    healthcheck:
-      test: ['CMD', 'redis-cli', '--raw', 'incr', 'ping']
-      interval: 10s
-      timeout: 5s
-      retries: 5
-  postgres:
-    image: postgres:16
-    container_name: affine_postgres
-    restart: unless-stopped
-    volumes:
-      - ~/.affine/self-host/postgres:/var/lib/postgresql/data
-    healthcheck:
-      test: ['CMD-SHELL', 'pg_isready -U affine']
-      interval: 10s
-      timeout: 5s
-      retries: 5
-    environment:
-      POSTGRES_USER: affine
-      POSTGRES_PASSWORD: affine
-      POSTGRES_DB: affine
-      PGDATA: /var/lib/postgresql/data/pgdata
diff --git a/.github/workflows/build-images.yml b/.github/workflows/build-images.yml
index 644bbe5c0..32b6b88f4 100644
--- a/.github/workflows/build-images.yml
+++ b/.github/workflows/build-images.yml
@@ -13,31 +13,6 @@ permissions:
   packages: 'write'
 
 jobs:
-  build-server:
-    name: Build Server
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Setup Version
-        id: version
-        uses: ./.github/actions/setup-version
-      - name: Setup Node.js
-        uses: ./.github/actions/setup-node
-        with:
-          electron-install: false
-          extra-flags: workspaces focus @affine/server @types/affine__env
-      - name: Build Server
-        run: |
-          find packages/backend/server/src -type d -name "__tests__" -exec rm -rf {} +
-          rm -rf packages/backend/server/src/seed
-          yarn workspace @affine/server build
-      - name: Upload server dist
-        uses: actions/upload-artifact@v4
-        with:
-          name: server-dist
-          path: ./packages/backend/server/dist
-          if-no-files-found: error
-
   build-web:
     name: Build @affine/web
     runs-on: ubuntu-latest
@@ -143,7 +118,7 @@ jobs:
       matrix:
         targets:
           - name: x86_64-unknown-linux-gnu
-            file: server-native.node
+            file: server-native.x64.node
           - name: aarch64-unknown-linux-gnu
             file: server-native.arm64.node
           - name: armv7-unknown-linux-gnueabihf
@@ -164,11 +139,46 @@ jobs:
         with:
           target: ${{ matrix.targets.name }}
           package: '@affine/server-native'
+      - name: Rename ${{ matrix.targets.file }}
+        run: |
+          mv ./packages/backend/native/server-native.node ./packages/backend/native/${{ matrix.targets.file }}
       - name: Upload ${{ matrix.targets.file }}
         uses: actions/upload-artifact@v4
         with:
-          name: ${{ matrix.targets.file }}
-          path: ./packages/backend/native/server-native.node
+          name: server-native-${{ matrix.targets.file }}
+          path: ./packages/backend/native/${{ matrix.targets.file }}
+          if-no-files-found: error
+
+  build-server:
+    name: Build Server
+    runs-on: ubuntu-latest
+    needs:
+      - build-server-native
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Version
+        id: version
+        uses: ./.github/actions/setup-version
+      - name: Setup Node.js
+        uses: ./.github/actions/setup-node
+        with:
+          electron-install: false
+          extra-flags: workspaces focus @affine/server @types/affine__env
+      - name: Download server-native
+        uses: actions/download-artifact@v4
+        with:
+          pattern: server-native-*
+          merge-multiple: true
+          path: ./packages/backend/native
+      - name: List server-native files
+        run: ls -alh ./packages/backend/native
+      - name: Build Server
+        run: yarn workspace @affine/server build
+      - name: Upload server dist
+        uses: actions/upload-artifact@v4
+        with:
+          name: server-dist
+          path: ./packages/backend/server/dist
           if-no-files-found: error
 
   build-images:
@@ -179,7 +189,6 @@ jobs:
       - build-web
       - build-mobile
       - build-admin
-      - build-server-native
     steps:
       - uses: actions/checkout@v4
       - name: Download server dist
@@ -187,25 +196,6 @@ jobs:
         with:
           name: server-dist
           path: ./packages/backend/server/dist
-      - name: Download server-native.node
-        uses: actions/download-artifact@v4
-        with:
-          name: server-native.node
-          path: ./packages/backend/server
-      - name: Download server-native.node arm64
-        uses: actions/download-artifact@v4
-        with:
-          name: server-native.arm64.node
-          path: ./packages/backend/native
-      - name: Download server-native.node arm64
-        uses: actions/download-artifact@v4
-        with:
-          name: server-native.armv7.node
-          path: .
-      - name: move server-native files
-        run: |
-          mv ./packages/backend/native/server-native.node ./packages/backend/server/server-native.arm64.node
-          mv server-native.node ./packages/backend/server/server-native.armv7.node
       - name: Setup env
         run: |
           echo "GIT_SHORT_HASH=$(git rev-parse --short HEAD)" >> "$GITHUB_ENV"
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
index 008ed9051..34e1a8b40 100644
--- a/.github/workflows/build-test.yml
+++ b/.github/workflows/build-test.yml
@@ -582,7 +582,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Prepare Server Test Environment
         uses: ./.github/actions/server-test-env
@@ -644,7 +644,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Prepare Server Test Environment
         uses: ./.github/actions/server-test-env
@@ -885,7 +885,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Prepare Server Test Environment
         if: ${{ steps.check-blocksuite-update.outputs.skip != 'true' || steps.apifilter.outputs.changed == 'true' }}
@@ -982,7 +982,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Prepare Server Test Environment
         if: ${{ steps.check-blocksuite-update.outputs.skip != 'true' || steps.e2efilter.outputs.changed == 'true' }}
@@ -1077,7 +1077,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Download affine.linux-x64-gnu.node
         uses: actions/download-artifact@v4
diff --git a/.github/workflows/copilot-test.yml b/.github/workflows/copilot-test.yml
index 8e78b9585..c50420b68 100644
--- a/.github/workflows/copilot-test.yml
+++ b/.github/workflows/copilot-test.yml
@@ -73,7 +73,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Prepare Server Test Environment
         env:
@@ -142,7 +142,7 @@ jobs:
         uses: actions/download-artifact@v4
         with:
           name: server-native.node
-          path: ./packages/backend/server
+          path: ./packages/backend/native
 
       - name: Prepare Server Test Environment
         env:
diff --git a/package.json b/package.json
index c70596db6..b4a647148 100644
--- a/package.json
+++ b/package.json
@@ -58,7 +58,6 @@
     "@magic-works/i18n-codegen": "^0.6.1",
     "@playwright/test": "=1.51.1",
     "@smarttools/eslint-plugin-rxjs": "^1.0.8",
-    "@swc/core": "^1.10.1",
     "@taplo/cli": "^0.7.0",
     "@toeverything/infra": "workspace:*",
     "@types/eslint": "^9.6.1",
diff --git a/packages/backend/native/index.js b/packages/backend/native/index.js
index 7a9334462..5392699df 100644
--- a/packages/backend/native/index.js
+++ b/packages/backend/native/index.js
@@ -1,15 +1,14 @@
-import { createRequire } from 'node:module';
-
-const require = createRequire(import.meta.url);
-
 /** @type {import('.')} */
-const binding = require('./server-native.node');
+let binding;
+try {
+  binding = require('./server-native.node');
+} catch {
+  binding =
+    process.arch === 'arm64'
+      ? require('./server-native.arm64.node')
+      : process.arch === 'arm'
+        ? require('./server-native.armv7.node')
+        : require('./server-native.x64.node');
+}
 
-export const mergeUpdatesInApplyWay = binding.mergeUpdatesInApplyWay;
-export const verifyChallengeResponse = binding.verifyChallengeResponse;
-export const mintChallengeResponse = binding.mintChallengeResponse;
-export const getMime = binding.getMime;
-export const Tokenizer = binding.Tokenizer;
-export const fromModelName = binding.fromModelName;
-export const htmlSanitize = binding.htmlSanitize;
-export const parseDoc = binding.parseDoc;
+module.exports = binding;
diff --git a/packages/backend/native/package.json b/packages/backend/native/package.json
index d1182a222..dfa425256 100644
--- a/packages/backend/native/package.json
+++ b/packages/backend/native/package.json
@@ -4,7 +4,6 @@
   "engines": {
     "node": ">= 10.16.0 < 11 || >= 11.8.0"
   },
-  "type": "module",
   "main": "./index.js",
   "module": "./index.js",
   "types": "index.d.ts",
diff --git a/packages/backend/server/package.json b/packages/backend/server/package.json
index 190f11121..819b5848a 100644
--- a/packages/backend/server/package.json
+++ b/packages/backend/server/package.json
@@ -8,7 +8,7 @@
     "run-test": "./scripts/run-test.ts"
   },
   "scripts": {
-    "build": "tsc -b",
+    "build": "affine bundle -p @affine/server",
     "dev": "nodemon ./src/index.ts",
     "dev:mail": "email dev -d src/mails",
     "test": "ava --concurrency 1 --serial",
@@ -17,14 +17,16 @@
     "test:copilot:coverage": "c8 ava --timeout=5m \"src/__tests__/copilot-*.spec.ts\"",
     "e2e": "cross-env TEST_MODE=e2e ava --serial",
     "e2e:coverage": "cross-env TEST_MODE=e2e c8 ava --serial",
-    "data-migration": "cross-env NODE_ENV=development r ./src/data/index.ts",
+    "data-migration": "cross-env NODE_ENV=development SERVER_FLAVOR=script r ./src/index.ts",
     "init": "yarn prisma migrate dev && yarn data-migration run",
     "seed": "r ./src/seed/index.ts",
     "genconfig": "r ./scripts/genconfig.ts",
-    "predeploy": "yarn prisma migrate deploy && node --import ./scripts/register.js ./dist/data/index.js run",
+    "cli": "cross-env SERVER_FLAVOR=script node ./dist/main.js",
+    "predeploy": "yarn prisma migrate deploy && yarn cli run",
     "postinstall": "prisma generate"
   },
   "dependencies": {
+    "@affine/server-native": "workspace:*",
     "@ai-sdk/google": "^1.2.10",
     "@ai-sdk/openai": "^1.3.18",
     "@ai-sdk/perplexity": "^1.1.6",
@@ -72,6 +74,7 @@
     "ai": "^4.3.4",
     "bullmq": "^5.40.2",
     "cookie-parser": "^1.4.7",
+    "cross-env": "^7.0.3",
     "date-fns": "^4.0.0",
     "dotenv": "^16.4.7",
     "eventemitter2": "^6.4.9",
@@ -117,7 +120,6 @@
     "@affine-tools/cli": "workspace:*",
     "@affine-tools/utils": "workspace:*",
     "@affine/graphql": "workspace:*",
-    "@affine/server-native": "workspace:*",
     "@faker-js/faker": "^9.6.0",
     "@nestjs/testing": "patch:@nestjs/testing@npm%3A10.4.15#~/.yarn/patches/@nestjs-testing-npm-10.4.15-d591a1705a.patch",
     "@types/cookie-parser": "^1.4.8",
@@ -138,7 +140,6 @@
     "@types/supertest": "^6.0.2",
     "ava": "^6.2.0",
     "c8": "^10.1.3",
-    "cross-env": "^7.0.3",
     "nodemon": "^3.1.7",
     "react-email": "4.0.7",
     "sinon": "^20.0.0",
diff --git a/packages/backend/server/scripts/loader.js b/packages/backend/server/scripts/loader.js
deleted file mode 100644
index ce31fb509..000000000
--- a/packages/backend/server/scripts/loader.js
+++ /dev/null
@@ -1,11 +0,0 @@
-import { create, createEsmHooks } from 'ts-node';
-
-const service = create({
-  experimentalSpecifierResolution: 'node',
-  transpileOnly: true,
-  logError: true,
-  skipProject: true,
-});
-const hooks = createEsmHooks(service);
-
-export const resolve = hooks.resolve;
diff --git a/packages/backend/server/scripts/register.js b/packages/backend/server/scripts/register.js
deleted file mode 100644
index ce20ff536..000000000
--- a/packages/backend/server/scripts/register.js
+++ /dev/null
@@ -1,4 +0,0 @@
-import { register } from 'node:module';
-import { pathToFileURL } from 'node:url';
-
-register('./scripts/loader.js', pathToFileURL('./'));
diff --git a/packages/backend/server/src/__tests__/env.spec.ts b/packages/backend/server/src/__tests__/env.spec.ts
index cd7f317dc..970b464fd 100644
--- a/packages/backend/server/src/__tests__/env.spec.ts
+++ b/packages/backend/server/src/__tests__/env.spec.ts
@@ -111,7 +111,7 @@ test('should tell flavors correctly', t => {
     sync: true,
     renderer: true,
     doc: true,
-    script: true,
+    script: false,
   });
 
   process.env.SERVER_FLAVOR = 'graphql';
@@ -122,6 +122,15 @@ test('should tell flavors correctly', t => {
     doc: false,
     script: false,
   });
+
+  process.env.SERVER_FLAVOR = 'script';
+  t.deepEqual(new Env().flavors, {
+    graphql: false,
+    sync: false,
+    renderer: false,
+    doc: false,
+    script: true,
+  });
 });
 
 test('should tell selfhosted correctly', t => {
diff --git a/packages/backend/server/src/data/index.ts b/packages/backend/server/src/cli.ts
similarity index 57%
rename from packages/backend/server/src/data/index.ts
rename to packages/backend/server/src/cli.ts
index 3797a9bad..6e347a9c1 100644
--- a/packages/backend/server/src/data/index.ts
+++ b/packages/backend/server/src/cli.ts
@@ -1,16 +1,12 @@
 import { Logger } from '@nestjs/common';
 import { CommandFactory } from 'nest-commander';
 
-async function bootstrap() {
-  process.env.SERVER_FLAVOR = 'script';
+import { CliAppModule } from './data/app';
 
-  await import('../prelude');
-  const { CliAppModule } = await import('./app');
+export async function run() {
   await CommandFactory.run(CliAppModule, new Logger()).catch(e => {
     console.error(e);
     process.exit(1);
   });
   process.exit(0);
 }
-
-await bootstrap();
diff --git a/packages/backend/server/src/data/commands/create.ts b/packages/backend/server/src/data/commands/create.ts
index 504dc7e36..32ec68910 100644
--- a/packages/backend/server/src/data/commands/create.ts
+++ b/packages/backend/server/src/data/commands/create.ts
@@ -1,5 +1,5 @@
-import { writeFileSync } from 'node:fs';
-import { join } from 'node:path';
+import { appendFileSync, writeFileSync } from 'node:fs';
+import { join, parse } from 'node:path';
 import { fileURLToPath } from 'node:url';
 
 import { Logger } from '@nestjs/common';
@@ -45,15 +45,21 @@ export class CreateCommand extends CommandRunner {
 
     const timestamp = Date.now();
     const content = this.createScript(upperFirst(camelCase(name)) + timestamp);
-    const fileName = `${timestamp}-${kebabCase(name)}.ts`;
-    const filePath = join(
+    const migrationDir = join(
       fileURLToPath(import.meta.url),
-      '../../migrations',
-      fileName
+      '../../migrations'
     );
+    const fileName = `${timestamp}-${kebabCase(name)}.ts`;
+    const filePath = join(migrationDir, fileName);
 
     this.logger.log(`Creating ${fileName}...`);
     writeFileSync(filePath, content);
+    const indexFile = join(migrationDir, 'index.ts');
+    appendFileSync(
+      indexFile,
+      `export * from './${parse(fileName).name}';`,
+      'utf-8'
+    );
     this.logger.log(`Migration file created at ${filePath}`);
     this.logger.log('Done');
   }
diff --git a/packages/backend/server/src/data/commands/run.ts b/packages/backend/server/src/data/commands/run.ts
index 50f501602..5f318d40f 100644
--- a/packages/backend/server/src/data/commands/run.ts
+++ b/packages/backend/server/src/data/commands/run.ts
@@ -1,49 +1,28 @@
-import { readdirSync } from 'node:fs';
-import { join } from 'node:path';
-import { fileURLToPath, pathToFileURL } from 'node:url';
-
 import { Logger } from '@nestjs/common';
 import { ModuleRef } from '@nestjs/core';
 import { PrismaClient } from '@prisma/client';
 import { once } from 'lodash-es';
 import { Command, CommandRunner } from 'nest-commander';
 
+import * as migrations from '../migrations';
+
 interface Migration {
-  file: string;
   name: string;
   always?: boolean;
   up: (db: PrismaClient, injector: ModuleRef) => Promise<void>;
   down: (db: PrismaClient, injector: ModuleRef) => Promise<void>;
 }
 
-export const collectMigrations = once(async () => {
-  const folder = join(fileURLToPath(import.meta.url), '../../migrations');
-
-  const migrationFiles = readdirSync(folder)
-    .filter(desc =>
-      desc.endsWith(import.meta.url.endsWith('.ts') ? '.ts' : '.js')
-    )
-    .map(desc => join(folder, desc));
-
-  migrationFiles.sort((a, b) => a.localeCompare(b));
-
-  const migrations: Migration[] = await Promise.all(
-    migrationFiles.map(async file => {
-      return import(pathToFileURL(file).href).then(mod => {
-        const migration = mod[Object.keys(mod)[0]];
-
-        return {
-          file,
-          name: migration.name,
-          always: migration.always,
-          up: migration.up,
-          down: migration.down,
-        };
-      });
-    })
-  );
-
-  return migrations;
+export const collectMigrations = once(() => {
+  return Object.values(migrations).map(migration => {
+    return {
+      name: migration.name,
+      // @ts-expect-error optional
+      always: migration.always,
+      up: migration.up,
+      down: migration.down,
+    };
+  }) as Migration[];
 });
 
 @Command({
@@ -60,7 +39,7 @@ export class RunCommand extends CommandRunner {
   }
 
   override async run(): Promise<void> {
-    const migrations = await collectMigrations();
+    const migrations = collectMigrations();
     const done: Migration[] = [];
     for (const migration of migrations) {
       const exists = await this.db.dataMigration.count({
@@ -85,7 +64,7 @@ export class RunCommand extends CommandRunner {
   }
 
   async runOne(name: string) {
-    const migrations = await collectMigrations();
+    const migrations = collectMigrations();
     const migration = migrations.find(m => m.name === name);
 
     if (!migration) {
@@ -162,7 +141,7 @@ export class RevertCommand extends CommandRunner {
       throw new Error('A migration name is required');
     }
 
-    const migrations = await collectMigrations();
+    const migrations = collectMigrations();
 
     const migration = migrations.find(m => m.name === name);
 
diff --git a/packages/backend/server/src/data/migrations/index.ts b/packages/backend/server/src/data/migrations/index.ts
new file mode 100644
index 000000000..8b0906b45
--- /dev/null
+++ b/packages/backend/server/src/data/migrations/index.ts
@@ -0,0 +1,7 @@
+export * from './0001-refresh-features';
+export * from './1698398506533-guid';
+export * from './1703756315970-unamed-account';
+export * from './1721299086340-refresh-unnamed-user';
+export * from './1732861452428-migrate-invite-status';
+export * from './1733125339942-universal-subscription';
+export * from './1738590347632-feature-redundant';
diff --git a/packages/backend/server/src/env.ts b/packages/backend/server/src/env.ts
index c308e88d4..ea2a76b5e 100644
--- a/packages/backend/server/src/env.ts
+++ b/packages/backend/server/src/env.ts
@@ -102,7 +102,8 @@ export class Env implements AppEnv {
       sync: this.isFlavor(Flavor.Sync),
       renderer: this.isFlavor(Flavor.Renderer),
       doc: this.isFlavor(Flavor.Doc),
-      script: this.isFlavor(Flavor.Script),
+      // Script in a special flavor, return true only when it is set explicitly
+      script: this.FLAVOR === Flavor.Script,
     };
   }
 
diff --git a/packages/backend/server/src/index.ts b/packages/backend/server/src/index.ts
index a0354c8b0..42806bd65 100644
--- a/packages/backend/server/src/index.ts
+++ b/packages/backend/server/src/index.ts
@@ -1,20 +1,11 @@
 /// <reference types="./global.d.ts" />
 import './prelude';
 
-import { Logger } from '@nestjs/common';
+import { run as runCli } from './cli';
+import { run as runServer } from './server';
 
-import { createApp } from './app';
-import { Config, URLHelper } from './base';
-
-const app = await createApp();
-const config = app.get(Config);
-const url = app.get(URLHelper);
-const listeningHost = '0.0.0.0';
-
-await app.listen(config.server.port, listeningHost);
-
-const logger = new Logger('App');
-
-logger.log(`AFFiNE Server is running in [${env.DEPLOYMENT_TYPE}] mode`);
-logger.log(`Listening on http://${listeningHost}:${config.server.port}`);
-logger.log(`And the public server should be recognized as ${url.home}`);
+if (env.flavors.script) {
+  await runCli();
+} else {
+  await runServer();
+}
diff --git a/packages/backend/server/src/native.ts b/packages/backend/server/src/native.ts
index c41618b78..0bb8ebefa 100644
--- a/packages/backend/server/src/native.ts
+++ b/packages/backend/server/src/native.ts
@@ -1,17 +1,4 @@
-import { createRequire } from 'node:module';
-
-let serverNativeModule: typeof import('@affine/server-native');
-try {
-  serverNativeModule = await import('@affine/server-native');
-} catch {
-  const require = createRequire(import.meta.url);
-  serverNativeModule =
-    process.arch === 'arm64'
-      ? require('../server-native.arm64.node')
-      : process.arch === 'arm'
-        ? require('../server-native.armv7.node')
-        : require('../server-native.node');
-}
+import serverNativeModule from '@affine/server-native';
 
 export const mergeUpdatesInApplyWay = serverNativeModule.mergeUpdatesInApplyWay;
 
diff --git a/packages/backend/server/src/app.ts b/packages/backend/server/src/server.ts
similarity index 77%
rename from packages/backend/server/src/app.ts
rename to packages/backend/server/src/server.ts
index 50df53b98..35a6b4c1e 100644
--- a/packages/backend/server/src/app.ts
+++ b/packages/backend/server/src/server.ts
@@ -9,6 +9,7 @@ import {
   CloudThrottlerGuard,
   Config,
   GlobalExceptionFilter,
+  URLHelper,
 } from './base';
 import { SocketIoAdapter } from './base/websocket';
 import { AuthGuard } from './core/auth';
@@ -16,7 +17,7 @@ import { serverTimingAndCache } from './middleware/timing';
 
 const OneMB = 1024 * 1024;
 
-export async function createApp() {
+export async function run() {
   const { AppModule } = await import('./app.module');
 
   const app = await NestFactory.create<NestExpressApplication>(AppModule, {
@@ -28,7 +29,8 @@ export async function createApp() {
 
   app.useBodyParser('raw', { limit: 100 * OneMB });
 
-  app.useLogger(app.get(AFFiNELogger));
+  const logger = app.get(AFFiNELogger);
+  app.useLogger(logger);
   const config = app.get(Config);
 
   if (config.server.path) {
@@ -57,5 +59,12 @@ export async function createApp() {
   const adapter = new SocketIoAdapter(app);
   app.useWebSocketAdapter(adapter);
 
-  return app;
+  const url = app.get(URLHelper);
+  const listeningHost = '0.0.0.0';
+
+  await app.listen(config.server.port, listeningHost);
+
+  logger.log(`AFFiNE Server is running in [${env.DEPLOYMENT_TYPE}] mode`);
+  logger.log(`Listening on http://${listeningHost}:${config.server.port}`);
+  logger.log(`And the public server should be recognized as ${url.home}`);
 }
diff --git a/packages/backend/server/tsconfig.json b/packages/backend/server/tsconfig.json
index 26fc078e1..6997a939f 100644
--- a/packages/backend/server/tsconfig.json
+++ b/packages/backend/server/tsconfig.json
@@ -12,9 +12,9 @@
   },
   "include": ["./src"],
   "references": [
+    { "path": "../native" },
     { "path": "../../../tools/cli" },
     { "path": "../../../tools/utils" },
-    { "path": "../../common/graphql" },
-    { "path": "../native" }
+    { "path": "../../common/graphql" }
   ]
 }
diff --git a/packages/common/infra/package.json b/packages/common/infra/package.json
index b048806b3..db90fd0aa 100644
--- a/packages/common/infra/package.json
+++ b/packages/common/infra/package.json
@@ -34,7 +34,6 @@
   "devDependencies": {
     "@affine/templates": "workspace:*",
     "@emotion/react": "^11.14.0",
-    "@swc/core": "^1.10.1",
     "@testing-library/dom": "^10.4.0",
     "@testing-library/react": "^16.1.0",
     "@types/react": "^19.0.1",
diff --git a/packages/frontend/core/package.json b/packages/frontend/core/package.json
index a0847b362..34fc18f3f 100644
--- a/packages/frontend/core/package.json
+++ b/packages/frontend/core/package.json
@@ -84,7 +84,6 @@
     "zod": "^3.24.1"
   },
   "devDependencies": {
-    "@swc/core": "^1.10.1",
     "@testing-library/dom": "^10.4.0",
     "@testing-library/react": "^16.1.0",
     "@types/animejs": "^3.1.12",
diff --git a/tools/cli/bin/cli.js b/tools/cli/bin/cli.js
new file mode 100755
index 000000000..be4c9ecf2
--- /dev/null
+++ b/tools/cli/bin/cli.js
@@ -0,0 +1,5 @@
+import { spawnSync } from 'node:child_process';
+
+spawnSync('yarn', ['r', 'affine.ts', ...process.argv.slice(2)], {
+  stdio: 'inherit',
+});
diff --git a/tools/cli/package.json b/tools/cli/package.json
index 6b444993b..37988114f 100644
--- a/tools/cli/package.json
+++ b/tools/cli/package.json
@@ -4,6 +4,7 @@
   "type": "module",
   "private": true,
   "bin": {
+    "affine": "./bin/cli.js",
     "r": "./bin/runner.js"
   },
   "exports": {
@@ -21,6 +22,7 @@
     "@napi-rs/simple-git": "^0.1.19",
     "@perfsee/webpack": "^1.13.0",
     "@sentry/webpack-plugin": "^3.0.0",
+    "@swc/core": "^1.10.1",
     "@tailwindcss/postcss": "^4.0.0",
     "@vanilla-extract/webpack-plugin": "^2.3.15",
     "autoprefixer": "^10.4.20",
@@ -34,6 +36,7 @@
     "lodash-es": "^4.17.21",
     "mime-types": "^3.0.0",
     "mini-css-extract-plugin": "^2.9.2",
+    "node-loader": "^2.1.0",
     "postcss": "^8.4.49",
     "postcss-loader": "^8.1.1",
     "prettier": "^3.4.2",
diff --git a/tools/cli/src/bundle.ts b/tools/cli/src/bundle.ts
index df3194f55..ed786b360 100644
--- a/tools/cli/src/bundle.ts
+++ b/tools/cli/src/bundle.ts
@@ -10,12 +10,16 @@ import WebpackDevServer, {
 } from 'webpack-dev-server';
 
 import { Option, PackageCommand } from './command';
-import { createHTMLTargetConfig, createWorkerTargetConfig } from './webpack';
+import {
+  createHTMLTargetConfig,
+  createNodeTargetConfig,
+  createWorkerTargetConfig,
+} from './webpack';
 
-function getBundleConfigs(pkg: Package) {
+function getBaseWorkerConfigs(pkg: Package) {
   const core = new Package('@affine/core');
 
-  const workerConfigs = [
+  return [
     createWorkerTargetConfig(
       pkg,
       core.srcPath.join(
@@ -31,7 +35,9 @@ function getBundleConfigs(pkg: Package) {
       core.srcPath.join('blocksuite/extensions/turbo-painter.worker.ts').value
     ),
   ];
+}
 
+function getBundleConfigs(pkg: Package) {
   switch (pkg.name) {
     case '@affine/admin': {
       return [createHTMLTargetConfig(pkg, pkg.srcPath.join('index.tsx').value)];
@@ -40,6 +46,7 @@ function getBundleConfigs(pkg: Package) {
     case '@affine/mobile':
     case '@affine/ios':
     case '@affine/android': {
+      const workerConfigs = getBaseWorkerConfigs(pkg);
       workerConfigs.push(
         createWorkerTargetConfig(
           pkg,
@@ -58,6 +65,8 @@ function getBundleConfigs(pkg: Package) {
       ];
     }
     case '@affine/electron-renderer': {
+      const workerConfigs = getBaseWorkerConfigs(pkg);
+
       return [
         createHTMLTargetConfig(
           pkg,
@@ -78,10 +87,14 @@ function getBundleConfigs(pkg: Package) {
         ...workerConfigs,
       ];
     }
+    case '@affine/server': {
+      return [createNodeTargetConfig(pkg, pkg.srcPath.join('index.ts').value)];
+    }
   }
 
   throw new Error(`Unsupported package: ${pkg.name}`);
 }
+
 const IN_CI = !!process.env.CI;
 const httpProxyMiddlewareLogLevel = IN_CI ? 'silent' : 'error';
 
diff --git a/tools/cli/src/webpack/index.ts b/tools/cli/src/webpack/index.ts
index 5d8f5908e..5f45c6a0f 100644
--- a/tools/cli/src/webpack/index.ts
+++ b/tools/cli/src/webpack/index.ts
@@ -2,7 +2,7 @@ import { createRequire } from 'node:module';
 import path from 'node:path';
 
 import { getBuildConfig } from '@affine-tools/utils/build-config';
-import { ProjectRoot } from '@affine-tools/utils/path';
+import { Path, ProjectRoot } from '@affine-tools/utils/path';
 import { Package } from '@affine-tools/utils/workspace';
 import { PerfseePlugin } from '@perfsee/webpack';
 import { sentryWebpackPlugin } from '@sentry/webpack-plugin';
@@ -75,10 +75,7 @@ export function createHTMLTargetConfig(
     },
     entry,
     output: {
-      environment: {
-        module: true,
-        dynamicImport: true,
-      },
+      environment: { module: true, dynamicImport: true },
       filename: buildConfig.debug
         ? 'js/[name].js'
         : 'js/[name].[contenthash:8].js',
@@ -127,12 +124,7 @@ export function createHTMLTargetConfig(
       },
       //#region rules
       rules: [
-        {
-          test: /\.m?js?$/,
-          resolve: {
-            fullySpecified: false,
-          },
-        },
+        { test: /\.m?js?$/, resolve: { fullySpecified: false } },
         {
           test: /\.js$/,
           enforce: 'pre',
@@ -185,9 +177,7 @@ export function createHTMLTargetConfig(
                   target: 'es2022',
                   externalHelpers: false,
                   transform: {
-                    react: {
-                      runtime: 'automatic',
-                    },
+                    react: { runtime: 'automatic' },
                     useDefineForClassFields: false,
                     decoratorVersion: '2022-03',
                   },
@@ -200,18 +190,9 @@ export function createHTMLTargetConfig(
               test: /\.(png|jpg|gif|svg|webp|mp4|zip)$/,
               type: 'asset/resource',
             },
-            {
-              test: /\.(ttf|eot|woff|woff2)$/,
-              type: 'asset/resource',
-            },
-            {
-              test: /\.txt$/,
-              type: 'asset/source',
-            },
-            {
-              test: /\.inline\.svg$/,
-              type: 'asset/inline',
-            },
+            { test: /\.(ttf|eot|woff|woff2)$/, type: 'asset/resource' },
+            { test: /\.txt$/, type: 'asset/source' },
+            { test: /\.inline\.svg$/, type: 'asset/inline' },
             {
               test: /\.css$/,
               use: [
@@ -242,12 +223,7 @@ export function createHTMLTargetConfig(
                           ]
                         : [
                             cssnano({
-                              preset: [
-                                'default',
-                                {
-                                  convertValues: false,
-                                },
-                              ],
+                              preset: ['default', { convertValues: false }],
                             }),
                           ],
                     },
@@ -298,9 +274,7 @@ export function createHTMLTargetConfig(
         new WebpackS3Plugin(),
       !buildConfig.debug &&
         process.env.PERFSEE_TOKEN &&
-        new PerfseePlugin({
-          project: 'affine-toeverything',
-        }),
+        new PerfseePlugin({ project: 'affine-toeverything' }),
       process.env.SENTRY_AUTH_TOKEN &&
         process.env.SENTRY_ORG &&
         process.env.SENTRY_PROJECT &&
@@ -325,9 +299,7 @@ export function createHTMLTargetConfig(
     ]),
     //#endregion
 
-    stats: {
-      errorDetails: true,
-    },
+    stats: { errorDetails: true },
 
     //#region optimization
     optimization: {
@@ -339,12 +311,8 @@ export function createHTMLTargetConfig(
           extractComments: true,
           terserOptions: {
             ecma: 2020,
-            compress: {
-              unused: true,
-            },
-            mangle: {
-              keep_classnames: true,
-            },
+            compress: { unused: true },
+            mangle: { keep_classnames: true },
           },
         }),
       ],
@@ -353,9 +321,7 @@ export function createHTMLTargetConfig(
       usedExports: true,
       sideEffects: true,
       removeAvailableModules: true,
-      runtimeChunk: {
-        name: 'runtime',
-      },
+      runtimeChunk: { name: 'runtime' },
       splitChunks: {
         chunks: 'all',
         minSize: 1,
@@ -382,11 +348,7 @@ export function createHTMLTargetConfig(
             priority: -10,
             reuseExistingChunk: true,
           },
-          default: {
-            minChunks: 2,
-            priority: -20,
-            reuseExistingChunk: true,
-          },
+          default: { minChunks: 2, priority: -20, reuseExistingChunk: true },
           styles: {
             name: 'styles',
             type: 'css/mini-extract',
@@ -416,9 +378,7 @@ export function createWorkerTargetConfig(
       outputModule: false,
       syncWebAssembly: true,
     },
-    entry: {
-      [workerName]: entry,
-    },
+    entry: { [workerName]: entry },
     output: {
       filename: `js/${workerName}-${buildConfig.appVersion}.worker.js`,
       path: pkg.distPath.value,
@@ -432,14 +392,9 @@ export function createWorkerTargetConfig(
     devtool: buildConfig.debug ? 'cheap-module-source-map' : 'source-map',
     resolve: {
       symlinks: true,
-      extensionAlias: {
-        '.js': ['.js', '.ts'],
-        '.mjs': ['.mjs', '.mts'],
-      },
+      extensionAlias: { '.js': ['.js', '.ts'], '.mjs': ['.mjs', '.mts'] },
       extensions: ['.js', '.ts'],
-      alias: {
-        yjs: ProjectRoot.join('node_modules', 'yjs').value,
-      },
+      alias: { yjs: ProjectRoot.join('node_modules', 'yjs').value },
     },
 
     module: {
@@ -454,12 +409,7 @@ export function createWorkerTargetConfig(
         },
       },
       rules: [
-        {
-          test: /\.m?js?$/,
-          resolve: {
-            fullySpecified: false,
-          },
-        },
+        { test: /\.m?js?$/, resolve: { fullySpecified: false } },
         {
           test: /\.js$/,
           enforce: 'pre',
@@ -508,9 +458,7 @@ export function createWorkerTargetConfig(
           {} as Record<string, string>
         )
       ),
-      new webpack.optimize.LimitChunkCountPlugin({
-        maxChunks: 1,
-      }),
+      new webpack.optimize.LimitChunkCountPlugin({ maxChunks: 1 }),
       process.env.SENTRY_AUTH_TOKEN &&
         process.env.SENTRY_ORG &&
         process.env.SENTRY_PROJECT &&
@@ -520,9 +468,7 @@ export function createWorkerTargetConfig(
           authToken: process.env.SENTRY_AUTH_TOKEN,
         }),
     ]),
-    stats: {
-      errorDetails: true,
-    },
+    stats: { errorDetails: true },
     optimization: {
       minimize: !buildConfig.debug,
       minimizer: [
@@ -532,12 +478,8 @@ export function createWorkerTargetConfig(
           extractComments: true,
           terserOptions: {
             ecma: 2020,
-            compress: {
-              unused: true,
-            },
-            mangle: {
-              keep_classnames: true,
-            },
+            compress: { unused: true },
+            mangle: { keep_classnames: true },
           },
         }),
       ],
@@ -549,8 +491,120 @@ export function createWorkerTargetConfig(
       runtimeChunk: false,
       splitChunks: false,
     },
-    performance: {
-      hints: false,
-    },
+    performance: { hints: false },
+  };
+}
+
+export function createNodeTargetConfig(
+  pkg: Package,
+  entry: string
+): Omit<webpack.Configuration, 'name'> & { name: string } {
+  return {
+    name: entry,
+    context: ProjectRoot.value,
+    experiments: {
+      topLevelAwait: true,
+      outputModule: pkg.packageJson.type === 'module',
+      syncWebAssembly: true,
+    },
+    entry: { index: entry },
+    output: {
+      filename: `main.js`,
+      path: pkg.distPath.value,
+      clean: true,
+      globalObject: 'globalThis',
+    },
+    target: ['node', 'es2022'],
+    externals: (data, callback) => {
+      if (
+        data.request &&
+        // import ... from 'module'
+        /^[a-zA-Z@]/.test(data.request) &&
+        // not workspace deps
+        !pkg.deps.some(dep => data.request!.startsWith(dep.name))
+      ) {
+        callback(null, true);
+      } else {
+        callback(null, false);
+      }
+    },
+    externalsPresets: { node: true },
+    node: { __dirname: false, __filename: false },
+    mode: 'none',
+    devtool: 'source-map',
+    resolve: {
+      symlinks: true,
+      extensionAlias: { '.js': ['.js', '.ts'], '.mjs': ['.mjs', '.mts'] },
+      extensions: ['.js', '.ts', '.tsx', '.node'],
+      alias: { yjs: ProjectRoot.join('node_modules', 'yjs').value },
+    },
+    module: {
+      parser: {
+        javascript: { url: false, importMeta: false, createRequire: false },
+      },
+      rules: [
+        {
+          test: /\.js$/,
+          enforce: 'pre',
+          include: /@blocksuite/,
+          use: ['source-map-loader'],
+        },
+        {
+          test: /\.node$/,
+          loader: Path.dir(import.meta.url).join('node-loader.js').value,
+        },
+        {
+          test: /\.tsx?$/,
+          exclude: /node_modules/,
+          loader: 'swc-loader',
+          options: {
+            // https://swc.rs/docs/configuring-swc/
+            jsc: {
+              preserveAllComments: true,
+              parser: {
+                syntax: 'typescript',
+                dynamicImport: true,
+                topLevelAwait: true,
+                tsx: true,
+                decorators: true,
+              },
+              target: 'es2022',
+              externalHelpers: false,
+              transform: {
+                legacyDecorator: true,
+                decoratorMetadata: true,
+                react: { runtime: 'automatic' },
+              },
+            },
+            sourceMaps: true,
+            inlineSourcesContent: true,
+          },
+        },
+      ],
+    },
+    plugins: compact([
+      new webpack.optimize.LimitChunkCountPlugin({ maxChunks: 1 }),
+      new webpack.IgnorePlugin({
+        checkResource(resource) {
+          const lazyImports = [
+            '@nestjs/microservices',
+            '@nestjs/websockets/socket-module',
+            '@apollo/subgraph',
+            '@apollo/gateway',
+            '@as-integrations/fastify',
+            'ts-morph',
+            'class-validator',
+            'class-transformer',
+          ];
+          return lazyImports.some(lazyImport =>
+            resource.startsWith(lazyImport)
+          );
+        },
+      }),
+    ]),
+    stats: { errorDetails: true },
+    optimization: { nodeEnv: false },
+    performance: { hints: false },
+    ignoreWarnings: [/^(?!CriticalDependenciesWarning$)/],
   };
 }
diff --git a/tools/cli/src/webpack/node-loader.js b/tools/cli/src/webpack/node-loader.js
new file mode 100644
index 000000000..124a4cb50
--- /dev/null
+++ b/tools/cli/src/webpack/node-loader.js
@@ -0,0 +1,18 @@
+import { parse } from 'node:path';
+
+export const raw = true;
+/**
+ * @type {import('webpack').LoaderDefinitionFunction}
+ */
+export default function loader(content) {
+  const name = parse(this.resourcePath).base;
+  this.emitFile(name, content);
+
+  return `
+    import { createRequire } from 'node:module'
+
+    const require = createRequire(import.meta.url)
+    const binding = require('./${name}')
+    export default binding
+  `;
+}
diff --git a/tools/utils/src/types.ts b/tools/utils/src/types.ts
index 9a7fd1cc2..0a72e4641 100644
--- a/tools/utils/src/types.ts
+++ b/tools/utils/src/types.ts
@@ -8,13 +8,12 @@ export interface YarnWorkspaceItem {
 
 export interface CommonPackageJsonContent {
   name: string;
+  type?: 'module' | 'commonjs';
   version: string;
   private?: boolean;
   dependencies?: { [key: string]: string };
   devDependencies?: { [key: string]: string };
   scripts?: { [key: string]: string };
   main?: string;
-  exports?: {
-    [key: string]: string;
-  };
+  exports?: { [key: string]: string | { [key: string]: string } };
 }
diff --git a/tools/utils/src/workspace.gen.ts b/tools/utils/src/workspace.gen.ts
index 96ec62f35..1344ca7ad 100644
--- a/tools/utils/src/workspace.gen.ts
+++ b/tools/utils/src/workspace.gen.ts
@@ -963,10 +963,10 @@ export const PackageList = [
     location: 'packages/backend/server',
     name: '@affine/server',
     workspaceDependencies: [
+      'packages/backend/native',
       'tools/cli',
       'tools/utils',
       'packages/common/graphql',
-      'packages/backend/native',
     ],
   },
   {
diff --git a/yarn.lock b/yarn.lock
index c930f805b..b449b7d2e 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -122,6 +122,7 @@ __metadata:
     "@napi-rs/simple-git": "npm:^0.1.19"
     "@perfsee/webpack": "npm:^1.13.0"
     "@sentry/webpack-plugin": "npm:^3.0.0"
+    "@swc/core": "npm:^1.10.1"
     "@tailwindcss/postcss": "npm:^4.0.0"
     "@types/lodash-es": "npm:^4.17.12"
     "@types/mime-types": "npm:^2.1.4"
@@ -139,6 +140,7 @@ __metadata:
     lodash-es: "npm:^4.17.21"
     mime-types: "npm:^3.0.0"
     mini-css-extract-plugin: "npm:^2.9.2"
+    node-loader: "npm:^2.1.0"
     postcss: "npm:^8.4.49"
     postcss-loader: "npm:^8.1.1"
     prettier: "npm:^3.4.2"
@@ -155,6 +157,7 @@ __metadata:
     webpack-dev-server: "npm:^5.2.0"
     webpack-merge: "npm:^6.0.1"
   bin:
+    affine: ./bin/cli.js
     r: ./bin/runner.js
   languageName: unknown
   linkType: soft
@@ -417,7 +420,6 @@ __metadata:
     "@radix-ui/react-slot": "npm:^1.1.1"
     "@radix-ui/react-toolbar": "npm:^1.1.1"
     "@sentry/react": "npm:^9.2.0"
-    "@swc/core": "npm:^1.10.1"
     "@testing-library/dom": "npm:^10.4.0"
     "@testing-library/react": "npm:^16.1.0"
     "@toeverything/infra": "workspace:*"
@@ -760,7 +762,6 @@ __metadata:
     "@magic-works/i18n-codegen": "npm:^0.6.1"
     "@playwright/test": "npm:=1.51.1"
     "@smarttools/eslint-plugin-rxjs": "npm:^1.0.8"
-    "@swc/core": "npm:^1.10.1"
     "@taplo/cli": "npm:^0.7.0"
     "@toeverything/infra": "workspace:*"
     "@types/eslint": "npm:^9.6.1"
@@ -14286,7 +14287,6 @@ __metadata:
     "@affine/templates": "workspace:*"
     "@emotion/react": "npm:^11.14.0"
     "@preact/signals-core": "npm:^1.8.0"
-    "@swc/core": "npm:^1.10.1"
     "@testing-library/dom": "npm:^10.4.0"
     "@testing-library/react": "npm:^16.1.0"
     "@types/react": "npm:^19.0.1"
@@ -25152,7 +25152,7 @@ __metadata:
   languageName: node
   linkType: hard
 
-"loader-utils@npm:^2.0.0":
+"loader-utils@npm:^2.0.0, loader-utils@npm:^2.0.3":
   version: 2.0.4
   resolution: "loader-utils@npm:2.0.4"
   dependencies:
@@ -27414,6 +27414,17 @@ __metadata:
   languageName: node
   linkType: hard
 
+"node-loader@npm:^2.1.0":
+  version: 2.1.0
+  resolution: "node-loader@npm:2.1.0"
+  dependencies:
+    loader-utils: "npm:^2.0.3"
+  peerDependencies:
+    webpack: ^5.0.0
+  checksum: 10/d2f20b1e0f946055fcbbf365c3927ffecfff9aee3b5cc2d71e45229ca27010267d3d6fdea04dcb7c0bc7ce9b87878105b8c1d15c05065c813b5c8ec5ef1fb4d1
+  languageName: node
+  linkType: hard
+
 "node-releases@npm:^2.0.19":
   version: 2.0.19
   resolution: "node-releases@npm:2.0.19"