diff --git a/.eslintrc.js b/.eslintrc.js
index 44b3a670a..20d1fe1f7 100644
--- a/.eslintrc.js
+++ b/.eslintrc.js
@@ -31,6 +31,11 @@ const createPattern = packageName => [
     message: 'Use `useNavigateHelper` instead',
     importNames: ['useNavigate'],
   },
+  {
+    group: ['yjs'],
+    message: 'Do not use this API because it has a bug',
+    importNames: ['mergeUpdates'],
+  },
 ];
 
 const allPackages = [
@@ -155,6 +160,11 @@ const config = {
             message: 'Use `useNavigateHelper` instead',
             importNames: ['useNavigate'],
           },
+          {
+            group: ['yjs'],
+            message: 'Do not use this API because it has a bug',
+            importNames: ['mergeUpdates'],
+          },
         ],
       },
     ],
diff --git a/apps/core/src/components/blocksuite/workspace-header/header-right-items/editor-option-menu.tsx b/apps/core/src/components/blocksuite/workspace-header/header-right-items/editor-option-menu.tsx
index 9e95f1d86..69f03a713 100644
--- a/apps/core/src/components/blocksuite/workspace-header/header-right-items/editor-option-menu.tsx
+++ b/apps/core/src/components/blocksuite/workspace-header/header-right-items/editor-option-menu.tsx
@@ -24,7 +24,7 @@ import { currentPageIdAtom } from '@toeverything/infra/atom';
 import { useAtom, useAtomValue, useSetAtom } from 'jotai';
 import { useCallback, useState } from 'react';
 import { useParams } from 'react-router-dom';
-import * as Y from 'yjs';
+import { applyUpdate, encodeStateAsUpdate } from 'yjs';
 
 import { pageSettingFamily, setPageModeAtom } from '../../../../atoms';
 import { useBlockSuiteMetaHelper } from '../../../../hooks/affine/use-block-suite-meta-helper';
@@ -35,6 +35,7 @@ import { HeaderDropDownButton } from '../../../pure/header-drop-down-button';
 import { usePageHelper } from '../../block-suite-page-list/utils';
 import { LanguageMenu } from './language-menu';
 import { MenuThemeModeSwitch } from './theme-mode-switch';
+
 const CommonMenu = () => {
   const content = (
     <div
@@ -117,8 +118,8 @@ export const PageMenu = ({ rename }: PageMenuProps) => {
     const currentPageMeta = currentPage.meta;
     const newPage = createPage();
     await newPage.waitForLoaded();
-    const update = Y.encodeStateAsUpdate(currentPage.spaceDoc);
-    Y.applyUpdate(newPage.spaceDoc, update);
+    const update = encodeStateAsUpdate(currentPage.spaceDoc);
+    applyUpdate(newPage.spaceDoc, update);
     setPageMeta(newPage.id, {
       tags: currentPageMeta.tags,
       favorite: currentPageMeta.favorite,
diff --git a/apps/electron/src/helper/db/__tests__/migration.spec.ts b/apps/electron/src/helper/db/__tests__/migration.spec.ts
index 06bf760c8..b066b78be 100644
--- a/apps/electron/src/helper/db/__tests__/migration.spec.ts
+++ b/apps/electron/src/helper/db/__tests__/migration.spec.ts
@@ -2,7 +2,7 @@ import path from 'node:path';
 
 import { SqliteConnection } from '@affine/native';
 import { afterEach, describe, expect, it, vi } from 'vitest';
-import * as Y from 'yjs';
+import { applyUpdate, Doc as YDoc } from 'yjs';
 
 import { removeWithRetry } from '../../../../tests/utils';
 import { copyToTemp, migrateToSubdocAndReplaceDatabase } from '../migration';
@@ -41,14 +41,14 @@ describe('migrateToSubdocAndReplaceDatabase', () => {
     expect(subdocUpdate).toBeDefined();
 
     // apply updates
-    const rootDoc = new Y.Doc();
-    Y.applyUpdate(rootDoc, rootUpdate);
+    const rootDoc = new YDoc();
+    applyUpdate(rootDoc, rootUpdate);
 
     // check if root doc has one subdoc
     expect(rootDoc.subdocs.size).toBe(1);
 
     // populates subdoc
-    Y.applyUpdate(rootDoc.subdocs.values().next().value, subdocUpdate);
+    applyUpdate(rootDoc.subdocs.values().next().value, subdocUpdate);
 
     // check if root doc's meta is correct
     const meta = rootDoc.getMap('meta').toJSON();
@@ -59,9 +59,7 @@ describe('migrateToSubdocAndReplaceDatabase', () => {
     expect(pageMeta.title).toBe('Welcome to AFFiNEd');
 
     // get the subdoc through id
-    const subDoc = rootDoc
-      .getMap('spaces')
-      .get(`space:${pageMeta.id}`) as Y.Doc;
+    const subDoc = rootDoc.getMap('spaces').get(`space:${pageMeta.id}`) as YDoc;
     expect(subDoc).toEqual(rootDoc.subdocs.values().next().value);
 
     await db.close();
diff --git a/apps/electron/src/helper/db/__tests__/workspace-db-adapter.spec.ts b/apps/electron/src/helper/db/__tests__/workspace-db-adapter.spec.ts
index f261446f6..e44c2dbd4 100644
--- a/apps/electron/src/helper/db/__tests__/workspace-db-adapter.spec.ts
+++ b/apps/electron/src/helper/db/__tests__/workspace-db-adapter.spec.ts
@@ -3,7 +3,7 @@ import path from 'node:path';
 import fs from 'fs-extra';
 import { v4 } from 'uuid';
 import { afterEach, expect, test, vi } from 'vitest';
-import * as Y from 'yjs';
+import { Doc as YDoc, encodeStateAsUpdate } from 'yjs';
 
 import { removeWithRetry } from '../../../../tests/utils';
 import { dbSubjects } from '../subjects';
@@ -21,18 +21,18 @@ afterEach(async () => {
   await removeWithRetry(tmpDir);
 });
 
-let testYDoc: Y.Doc;
-let testYSubDoc: Y.Doc;
+let testYDoc: YDoc;
+let testYSubDoc: YDoc;
 
 function getTestUpdates() {
-  testYDoc = new Y.Doc();
+  testYDoc = new YDoc();
   const yText = testYDoc.getText('test');
   yText.insert(0, 'hello');
 
-  testYSubDoc = new Y.Doc();
+  testYSubDoc = new YDoc();
   testYDoc.getMap('subdocs').set('test-subdoc', testYSubDoc);
 
-  const updates = Y.encodeStateAsUpdate(testYDoc);
+  const updates = encodeStateAsUpdate(testYDoc);
 
   return updates;
 }
@@ -41,7 +41,7 @@ function getTestSubDocUpdates() {
   const yText = testYSubDoc.getText('test');
   yText.insert(0, 'hello');
 
-  const updates = Y.encodeStateAsUpdate(testYSubDoc);
+  const updates = encodeStateAsUpdate(testYSubDoc);
 
   return updates;
 }
diff --git a/apps/electron/src/helper/db/merge-update.ts b/apps/electron/src/helper/db/merge-update.ts
index b93467d9d..b17b92001 100644
--- a/apps/electron/src/helper/db/merge-update.ts
+++ b/apps/electron/src/helper/db/merge-update.ts
@@ -1,11 +1,11 @@
-import * as Y from 'yjs';
+import { applyUpdate, Doc as YDoc, encodeStateAsUpdate, transact } from 'yjs';
 
 export function mergeUpdate(updates: Uint8Array[]) {
-  const yDoc = new Y.Doc();
-  Y.transact(yDoc, () => {
+  const yDoc = new YDoc();
+  transact(yDoc, () => {
     for (const update of updates) {
-      Y.applyUpdate(yDoc, update);
+      applyUpdate(yDoc, update);
     }
   });
-  return Y.encodeStateAsUpdate(yDoc);
+  return encodeStateAsUpdate(yDoc);
 }
diff --git a/apps/electron/src/helper/db/migration.ts b/apps/electron/src/helper/db/migration.ts
index 2d50b2c5f..fe07c524c 100644
--- a/apps/electron/src/helper/db/migration.ts
+++ b/apps/electron/src/helper/db/migration.ts
@@ -4,7 +4,7 @@ import { migrateToSubdoc } from '@affine/env/blocksuite';
 import { SqliteConnection } from '@affine/native';
 import fs from 'fs-extra';
 import { nanoid } from 'nanoid';
-import * as Y from 'yjs';
+import { applyUpdate, Doc as YDoc, encodeStateAsUpdate } from 'yjs';
 
 import { mainRPC } from '../main-rpc';
 
@@ -13,11 +13,11 @@ export const migrateToSubdocAndReplaceDatabase = async (path: string) => {
   await db.connect();
 
   const rows = await db.getAllUpdates();
-  const originalDoc = new Y.Doc();
+  const originalDoc = new YDoc();
 
   // 1. apply all updates to the root doc
   rows.forEach(row => {
-    Y.applyUpdate(originalDoc, row.data);
+    applyUpdate(originalDoc, row.data);
   });
 
   // 2. migrate using migrateToSubdoc
@@ -40,10 +40,10 @@ export const copyToTemp = async (path: string) => {
 
 async function replaceRows(
   db: SqliteConnection,
-  doc: Y.Doc,
+  doc: YDoc,
   isRoot: boolean
 ): Promise<void> {
-  const migratedUpdates = Y.encodeStateAsUpdate(doc);
+  const migratedUpdates = encodeStateAsUpdate(doc);
   const docId = isRoot ? undefined : doc.guid;
   const rows = [{ data: migratedUpdates, docId: docId }];
   await db.replaceUpdates(docId, rows);
diff --git a/apps/electron/src/helper/db/secondary-db.ts b/apps/electron/src/helper/db/secondary-db.ts
index 7c0be42e6..265aca105 100644
--- a/apps/electron/src/helper/db/secondary-db.ts
+++ b/apps/electron/src/helper/db/secondary-db.ts
@@ -2,7 +2,7 @@ import assert from 'node:assert';
 
 import type { InsertRow } from '@affine/native';
 import { debounce } from 'lodash-es';
-import * as Y from 'yjs';
+import { applyUpdate, Doc as YDoc } from 'yjs';
 
 import { logger } from '../logger';
 import type { YOrigin } from '../type';
@@ -16,7 +16,7 @@ const FLUSH_MAX_WAIT_TIME = 10000;
 // todo: trim db when it is too big
 export class SecondaryWorkspaceSQLiteDB extends BaseSQLiteAdapter {
   role = 'secondary';
-  yDoc = new Y.Doc();
+  yDoc = new YDoc();
   firstConnected = false;
   destroyed = false;
 
@@ -165,7 +165,7 @@ export class SecondaryWorkspaceSQLiteDB extends BaseSQLiteAdapter {
       }
     };
 
-    const onSubdocs = ({ added }: { added: Set<Y.Doc> }) => {
+    const onSubdocs = ({ added }: { added: Set<YDoc> }) => {
       added.forEach(subdoc => {
         this.setupListener(subdoc.guid);
       });
@@ -214,7 +214,7 @@ export class SecondaryWorkspaceSQLiteDB extends BaseSQLiteAdapter {
   ) => {
     const doc = this.getDoc(docId);
     if (doc) {
-      Y.applyUpdate(this.yDoc, data, origin);
+      applyUpdate(this.yDoc, data, origin);
     } else {
       logger.warn(
         '[SecondaryWorkspaceSQLiteDB] applyUpdate: doc not found',
diff --git a/apps/electron/src/helper/db/workspace-db-adapter.ts b/apps/electron/src/helper/db/workspace-db-adapter.ts
index 63f1bbbb3..8eda459c4 100644
--- a/apps/electron/src/helper/db/workspace-db-adapter.ts
+++ b/apps/electron/src/helper/db/workspace-db-adapter.ts
@@ -1,7 +1,7 @@
 import type { InsertRow } from '@affine/native';
 import { debounce } from 'lodash-es';
 import { Subject } from 'rxjs';
-import * as Y from 'yjs';
+import { applyUpdate, Doc as YDoc, encodeStateAsUpdate } from 'yjs';
 
 import { logger } from '../logger';
 import type { YOrigin } from '../type';
@@ -13,7 +13,7 @@ const TRIM_SIZE = 500;
 
 export class WorkspaceSQLiteDB extends BaseSQLiteAdapter {
   role = 'primary';
-  yDoc = new Y.Doc();
+  yDoc = new YDoc();
   firstConnected = false;
 
   update$ = new Subject<void>();
@@ -78,7 +78,7 @@ export class WorkspaceSQLiteDB extends BaseSQLiteAdapter {
       doc.subdocs.forEach(subdoc => {
         this.setupListener(subdoc.guid);
       });
-      const onSubdocs = ({ added }: { added: Set<Y.Doc> }) => {
+      const onSubdocs = ({ added }: { added: Set<YDoc> }) => {
         logger.info('onSubdocs', this.workspaceId, docId, added);
         added.forEach(subdoc => {
           this.setupListener(subdoc.guid);
@@ -126,7 +126,7 @@ export class WorkspaceSQLiteDB extends BaseSQLiteAdapter {
   getDocAsUpdates = (docId?: string) => {
     const doc = docId ? this.getDoc(docId) : this.yDoc;
     if (doc) {
-      return Y.encodeStateAsUpdate(doc);
+      return encodeStateAsUpdate(doc);
     }
     return null;
   };
@@ -144,7 +144,7 @@ export class WorkspaceSQLiteDB extends BaseSQLiteAdapter {
     // yjs-idb will always trim the db for the first time after DB is loaded
     const doc = this.getDoc(docId);
     if (doc) {
-      Y.applyUpdate(doc, data, origin);
+      applyUpdate(doc, data, origin);
     } else {
       logger.warn('[WorkspaceSQLiteDB] applyUpdate: doc not found', docId);
     }
diff --git a/packages/env/src/__tests__/subdoc-migration.spec.ts b/packages/env/src/__tests__/subdoc-migration.spec.ts
index 7b99f7d59..882ee57bb 100644
--- a/packages/env/src/__tests__/subdoc-migration.spec.ts
+++ b/packages/env/src/__tests__/subdoc-migration.spec.ts
@@ -2,7 +2,8 @@ import { readFileSync } from 'fs';
 import { dirname, resolve } from 'path';
 import { fileURLToPath } from 'url';
 import { describe, expect, test } from 'vitest';
-import * as Y from 'yjs';
+import type { Array as YArray, Map as YMap } from 'yjs';
+import { applyUpdate, Doc } from 'yjs';
 
 import { migrateToSubdoc } from '../blocksuite/index.js';
 
@@ -11,8 +12,8 @@ const fixturePath = resolve(
   'workspace.ydoc'
 );
 const yDocBuffer = readFileSync(fixturePath);
-const doc = new Y.Doc();
-Y.applyUpdate(doc, new Uint8Array(yDocBuffer));
+const doc = new Doc();
+applyUpdate(doc, new Uint8Array(yDocBuffer));
 const migratedDoc = migrateToSubdoc(doc);
 
 describe('subdoc', () => {
@@ -23,8 +24,8 @@ describe('subdoc', () => {
     for (let i = 0; i < length; i++) {
       binary[i] = (json as any)[i];
     }
-    const doc = new Y.Doc();
-    Y.applyUpdate(doc, binary);
+    const doc = new Doc();
+    applyUpdate(doc, binary);
     {
       // invoke data
       doc.getMap('space:hello-world');
@@ -32,7 +33,7 @@ describe('subdoc', () => {
     }
     const blocks = doc.getMap('space:hello-world').toJSON();
     const newDoc = migrateToSubdoc(doc);
-    const subDoc = newDoc.getMap('spaces').get('space:hello-world') as Y.Doc;
+    const subDoc = newDoc.getMap('spaces').get('space:hello-world') as Doc;
     const data = (subDoc.toJSON() as any).blocks;
     Object.keys(data).forEach(id => {
       if (id === 'xyWNqindHH') {
@@ -50,23 +51,23 @@ describe('subdoc', () => {
 
   test('Test fixture should be set correctly', () => {
     const meta = doc.getMap('space:meta');
-    const versions = meta.get('versions') as Y.Map<unknown>;
+    const versions = meta.get('versions') as YMap<unknown>;
     expect(versions.get('affine:code')).toBeTypeOf('number');
   });
 
   test('Meta data should be migrated correctly', () => {
     const originalMeta = doc.getMap('space:meta');
-    const originalVersions = originalMeta.get('versions') as Y.Map<unknown>;
+    const originalVersions = originalMeta.get('versions') as YMap<unknown>;
 
     const meta = migratedDoc.getMap('meta');
-    const blockVersions = meta.get('blockVersions') as Y.Map<unknown>;
+    const blockVersions = meta.get('blockVersions') as YMap<unknown>;
 
     expect(meta.get('workspaceVersion')).toBe(1);
     expect(blockVersions.get('affine:code')).toBe(
       originalVersions.get('affine:code')
     );
-    expect((meta.get('pages') as Y.Array<unknown>).length).toBe(
-      (originalMeta.get('pages') as Y.Array<unknown>).length
+    expect((meta.get('pages') as YArray<unknown>).length).toBe(
+      (originalMeta.get('pages') as YArray<unknown>).length
     );
 
     expect(blockVersions.get('affine:embed')).toBeUndefined();
diff --git a/packages/env/src/blocksuite/subdoc-migration.ts b/packages/env/src/blocksuite/subdoc-migration.ts
index 251f948fd..f3feb871d 100644
--- a/packages/env/src/blocksuite/subdoc-migration.ts
+++ b/packages/env/src/blocksuite/subdoc-migration.ts
@@ -1,5 +1,5 @@
 import type { Schema } from '@blocksuite/store';
-import * as Y from 'yjs';
+import { Array as YArray, Doc as YDoc, Map as YMap } from 'yjs';
 
 type XYWH = [number, number, number, number];
 
@@ -7,10 +7,10 @@ function deserializeXYWH(xywh: string): XYWH {
   return JSON.parse(xywh) as XYWH;
 }
 
-function migrateDatabase(data: Y.Map<unknown>) {
+function migrateDatabase(data: YMap<unknown>) {
   data.delete('prop:mode');
-  data.set('prop:views', new Y.Array());
-  const columns = (data.get('prop:columns') as Y.Array<unknown>).toJSON() as {
+  data.set('prop:views', new YArray());
+  const columns = (data.get('prop:columns') as YArray<unknown>).toJSON() as {
     id: string;
     name: string;
     hide: boolean;
@@ -31,7 +31,7 @@ function migrateDatabase(data: Y.Map<unknown>) {
       mode: 'table',
     },
   ];
-  const cells = (data.get('prop:cells') as Y.Map<unknown>).toJSON() as Record<
+  const cells = (data.get('prop:cells') as YMap<unknown>).toJSON() as Record<
     string,
     Record<
       string,
@@ -90,7 +90,7 @@ function migrateDatabase(data: Y.Map<unknown>) {
 
 function runBlockMigration(
   flavour: string,
-  data: Y.Map<unknown>,
+  data: YMap<unknown>,
   version: number
 ) {
   if (flavour === 'affine:frame') {
@@ -99,12 +99,12 @@ function runBlockMigration(
   }
   if (flavour === 'affine:surface' && version <= 3) {
     if (data.has('elements')) {
-      const elements = data.get('elements') as Y.Map<unknown>;
+      const elements = data.get('elements') as YMap<unknown>;
       migrateSurface(elements);
       data.set('prop:elements', elements.clone());
       data.delete('elements');
     } else {
-      data.set('prop:elements', new Y.Map());
+      data.set('prop:elements', new YMap());
     }
   }
   if (flavour === 'affine:embed') {
@@ -116,8 +116,8 @@ function runBlockMigration(
   }
 }
 
-function migrateSurface(data: Y.Map<unknown>) {
-  for (const [, value] of <IterableIterator<[string, Y.Map<unknown>]>>(
+function migrateSurface(data: YMap<unknown>) {
+  for (const [, value] of <IterableIterator<[string, YMap<unknown>]>>(
     data.entries()
   )) {
     if (value.get('type') === 'connector') {
@@ -126,7 +126,7 @@ function migrateSurface(data: Y.Map<unknown>) {
   }
 }
 
-function migrateSurfaceConnector(data: Y.Map<any>) {
+function migrateSurfaceConnector(data: YMap<any>) {
   let id = data.get('startElement')?.id;
   const controllers = data.get('controllers');
   const length = controllers.length;
@@ -164,7 +164,7 @@ function migrateSurfaceConnector(data: Y.Map<any>) {
   data.delete('xywh');
 }
 
-function updateBlockVersions(versions: Y.Map<number>) {
+function updateBlockVersions(versions: YMap<number>) {
   const frameVersion = versions.get('affine:frame');
   if (frameVersion !== undefined) {
     versions.set('affine:note', frameVersion);
@@ -181,12 +181,12 @@ function updateBlockVersions(versions: Y.Map<number>) {
   }
 }
 
-function migrateMeta(oldDoc: Y.Doc, newDoc: Y.Doc) {
+function migrateMeta(oldDoc: YDoc, newDoc: YDoc) {
   const originalMeta = oldDoc.getMap('space:meta');
-  const originalVersions = originalMeta.get('versions') as Y.Map<number>;
-  const originalPages = originalMeta.get('pages') as Y.Array<Y.Map<unknown>>;
+  const originalVersions = originalMeta.get('versions') as YMap<number>;
+  const originalPages = originalMeta.get('pages') as YArray<YMap<unknown>>;
   const meta = newDoc.getMap('meta');
-  const pages = new Y.Array();
+  const pages = new YArray();
   const blockVersions = originalVersions.clone();
 
   meta.set('workspaceVersion', 1);
@@ -196,7 +196,7 @@ function migrateMeta(oldDoc: Y.Doc, newDoc: Y.Doc) {
 
   updateBlockVersions(blockVersions);
   const mapList = originalPages.map(page => {
-    const map = new Y.Map();
+    const map = new YMap();
     Array.from(page.entries())
       .filter(([key]) => key !== 'subpageIds')
       .forEach(([key, value]) => {
@@ -207,16 +207,16 @@ function migrateMeta(oldDoc: Y.Doc, newDoc: Y.Doc) {
   pages.push(mapList);
 }
 
-function migrateBlocks(oldDoc: Y.Doc, newDoc: Y.Doc) {
+function migrateBlocks(oldDoc: YDoc, newDoc: YDoc) {
   const spaces = newDoc.getMap('spaces');
   const originalMeta = oldDoc.getMap('space:meta');
-  const originalVersions = originalMeta.get('versions') as Y.Map<number>;
-  const originalPages = originalMeta.get('pages') as Y.Array<Y.Map<unknown>>;
+  const originalVersions = originalMeta.get('versions') as YMap<number>;
+  const originalPages = originalMeta.get('pages') as YArray<YMap<unknown>>;
   originalPages.forEach(page => {
     const id = page.get('id') as string;
     const spaceId = id.startsWith('space:') ? id : `space:${id}`;
-    const originalBlocks = oldDoc.getMap(spaceId) as Y.Map<unknown>;
-    const subdoc = new Y.Doc();
+    const originalBlocks = oldDoc.getMap(spaceId) as YMap<unknown>;
+    const subdoc = new YDoc();
     spaces.set(spaceId, subdoc);
     const blocks = subdoc.getMap('blocks');
     Array.from(originalBlocks.entries()).forEach(([key, value]) => {
@@ -231,19 +231,19 @@ function migrateBlocks(oldDoc: Y.Doc, newDoc: Y.Doc) {
   });
 }
 
-export function migrateToSubdoc(doc: Y.Doc): Y.Doc {
+export function migrateToSubdoc(doc: YDoc): YDoc {
   const needMigration = Array.from(doc.getMap('space:meta').keys()).length > 0;
   if (!needMigration) {
     return doc;
   }
-  const output = new Y.Doc();
+  const output = new YDoc();
   migrateMeta(doc, output);
   migrateBlocks(doc, output);
   return output;
 }
 
-export async function migrateDatabaseBlockTo3(rootDoc: Y.Doc, schema: Schema) {
-  const spaces = rootDoc.getMap('spaces') as Y.Map<any>;
+export async function migrateDatabaseBlockTo3(rootDoc: YDoc, schema: Schema) {
+  const spaces = rootDoc.getMap('spaces') as YMap<any>;
   spaces.forEach(space => {
     schema.upgradePage(
       {
@@ -261,7 +261,7 @@ export async function migrateDatabaseBlockTo3(rootDoc: Y.Doc, schema: Schema) {
       space
     );
   });
-  const meta = rootDoc.getMap('meta') as Y.Map<unknown>;
-  const versions = meta.get('blockVersions') as Y.Map<number>;
+  const meta = rootDoc.getMap('meta') as YMap<unknown>;
+  const versions = meta.get('blockVersions') as YMap<number>;
   versions.set('affine:database', 3);
 }
diff --git a/packages/storage/__tests__/storage.spec.js b/packages/storage/__tests__/storage.spec.js
index 234bc2f86..263404468 100644
--- a/packages/storage/__tests__/storage.spec.js
+++ b/packages/storage/__tests__/storage.spec.js
@@ -2,13 +2,44 @@ import assert from 'node:assert';
 import { beforeEach, describe, test } from 'node:test';
 
 import { encoding } from 'lib0';
-import * as Y from 'yjs';
+import { applyUpdate, Doc } from 'yjs';
 
 import { Storage } from '../index.js';
 
 // update binary by y.doc.text('content').insert('hello world')
 // prettier-ignore
-let init = Buffer.from([1,1,160,238,169,240,10,0,4,1,7,99,111,110,116,101,110,116,11,104,101,108,108,111,32,119,111,114,108,100,0])
+let init = Buffer.from([
+  1,
+  1,
+  160,
+  238,
+  169,
+  240,
+  10,
+  0,
+  4,
+  1,
+  7,
+  99,
+  111,
+  110,
+  116,
+  101,
+  110,
+  116,
+  11,
+  104,
+  101,
+  108,
+  108,
+  111,
+  32,
+  119,
+  111,
+  114,
+  108,
+  100,
+  0])
 describe('Test jwst storage binding', () => {
   /** @type { Storage } */
   let storage;
@@ -48,8 +79,8 @@ describe('Test jwst storage binding', () => {
     const update = await storage.load(workspace.doc.guid);
     assert(update !== null);
 
-    const doc = new Y.Doc();
-    Y.applyUpdate(doc, update);
+    const doc = new Doc();
+    applyUpdate(doc, update);
 
     let text = doc.getText('content');
     assert.equal(text.toJSON(), 'hello world');
@@ -67,8 +98,8 @@ describe('Test jwst storage binding', () => {
     }
 
     const update2 = await storage.load(workspace.doc.guid);
-    const doc2 = new Y.Doc();
-    Y.applyUpdate(doc2, update2);
+    const doc2 = new Doc();
+    applyUpdate(doc2, update2);
 
     text = doc2.getText('content');
     assert.equal(text.toJSON(), 'hello my world!');
@@ -80,8 +111,8 @@ describe('Test jwst storage binding', () => {
     const update = await storage.load(workspace.doc.guid);
     assert(update !== null);
 
-    const doc = new Y.Doc();
-    Y.applyUpdate(doc, update);
+    const doc = new Doc();
+    applyUpdate(doc, update);
 
     let text = doc.getText('content');
     assert.equal(text.toJSON(), 'hello world');
@@ -103,8 +134,8 @@ describe('Test jwst storage binding', () => {
     }
 
     const update2 = await storage.load(workspace.doc.guid);
-    const doc2 = new Y.Doc();
-    Y.applyUpdate(doc2, update2);
+    const doc2 = new Doc();
+    applyUpdate(doc2, update2);
 
     text = doc2.getText('content');
     assert.equal(text.toJSON(), 'hello my world!');
diff --git a/packages/y-indexeddb/src/__tests__/index.spec.ts b/packages/y-indexeddb/src/__tests__/index.spec.ts
index d8fa487ba..0035c1280 100644
--- a/packages/y-indexeddb/src/__tests__/index.spec.ts
+++ b/packages/y-indexeddb/src/__tests__/index.spec.ts
@@ -435,15 +435,13 @@ describe('utils', () => {
   });
 
   test('overwrite binary', async () => {
-    await overwriteBinary('test', new Uint8Array([1, 2, 3]));
+    const doc = new Doc();
+    const map = doc.getMap();
+    map.set('1', 1);
+    await overwriteBinary('test', new Uint8Array(encodeStateAsUpdate(doc)));
     {
       const binary = await downloadBinary('test');
-      expect(binary).toEqual(new Uint8Array([1, 2, 3]));
-    }
-    await overwriteBinary('test', new Uint8Array([0, 0]));
-    {
-      const binary = await downloadBinary('test');
-      expect(binary).toEqual(new Uint8Array([0, 0]));
+      expect(binary).toEqual(new Uint8Array(encodeStateAsUpdate(doc)));
     }
   });
 });
diff --git a/packages/y-indexeddb/src/provider.ts b/packages/y-indexeddb/src/provider.ts
index 5cf984033..859d31877 100644
--- a/packages/y-indexeddb/src/provider.ts
+++ b/packages/y-indexeddb/src/provider.ts
@@ -6,7 +6,7 @@ import {
 import { assertExists } from '@blocksuite/global/utils';
 import { openDB } from 'idb';
 import type { Doc } from 'yjs';
-import { diffUpdate, mergeUpdates } from 'yjs';
+import { diffUpdate } from 'yjs';
 
 import {
   type BlockSuiteBinaryDB,
@@ -16,6 +16,7 @@ import {
   type UpdateMessage,
   upgradeDB,
 } from './shared';
+import { mergeUpdates } from './utils';
 
 let mergeCount = 500;
 
diff --git a/packages/y-indexeddb/src/utils.ts b/packages/y-indexeddb/src/utils.ts
index c1c3ae0cf..30a1a1df3 100644
--- a/packages/y-indexeddb/src/utils.ts
+++ b/packages/y-indexeddb/src/utils.ts
@@ -1,12 +1,20 @@
 import type { IDBPDatabase } from 'idb';
 import { openDB } from 'idb';
-import { mergeUpdates } from 'yjs';
+import { applyUpdate, Doc, encodeStateAsUpdate } from 'yjs';
 
 import type { BlockSuiteBinaryDB, OldYjsDB, UpdateMessage } from './shared';
 import { dbVersion, DEFAULT_DB_NAME, upgradeDB } from './shared';
 
 let allDb: IDBDatabaseInfo[];
 
+export function mergeUpdates(updates: Uint8Array[]) {
+  const doc = new Doc();
+  updates.forEach(update => {
+    applyUpdate(doc, update);
+  });
+  return encodeStateAsUpdate(doc);
+}
+
 async function databaseExists(name: string): Promise<boolean> {
   return new Promise(resolve => {
     const req = indexedDB.open(name);