diff --git a/blocksuite/affine/blocks/bookmark/src/__tests__/adapters/preprocessor.unit.spec.ts b/blocksuite/affine/blocks/bookmark/src/__tests__/adapters/preprocessor.unit.spec.ts
index 7dcbfb39b..3d1c8e90a 100644
--- a/blocksuite/affine/blocks/bookmark/src/__tests__/adapters/preprocessor.unit.spec.ts
+++ b/blocksuite/affine/blocks/bookmark/src/__tests__/adapters/preprocessor.unit.spec.ts
@@ -140,4 +140,16 @@ Some text in between
     `.trim();
     expect(footnoteUrlPreprocessor(input)).toBe(expected);
   });
+
+  it('should encode partial encoded URLs in footnote definitions', () => {
+    const input = `
+[^ref]: {"type":"url","url":"https://zh.wikipedia.org/zh-hans/%E5%B0%8F%E7%B1%B3SU7"}
+[^ref2]: {"type":"url","url":"https://www.dw.com/zh/%E5%B0%8F%E7%B1%B3%E9%A6%96%E6%AC%BE%E6%B1%BD%E8%BD%A6%E5%8F%91%E5%B8%83-su7%E8%B5%B7%E4%BB%B72159%E4%B8%87%E5%85%83/a-68693432"}
+  `.trim();
+    const expected = `
+[^ref]: {"type":"url","url":"https%3A%2F%2Fzh.wikipedia.org%2Fzh-hans%2F%25E5%25B0%258F%25E7%25B1%25B3SU7"}
+[^ref2]: {"type":"url","url":"https%3A%2F%2Fwww.dw.com%2Fzh%2F%25E5%25B0%258F%25E7%25B1%25B3%25E9%25A6%2596%25E6%25AC%25BE%25E6%25B1%25BD%25E8%25BD%25A6%25E5%258F%2591%25E5%25B8%2583-su7%25E8%25B5%25B7%25E4%25BB%25B72159%25E4%25B8%2587%25E5%2585%2583%2Fa-68693432"}
+    `.trim();
+    expect(footnoteUrlPreprocessor(input)).toBe(expected);
+  });
 });
diff --git a/blocksuite/affine/blocks/bookmark/src/adapters/markdown/preprocessor.ts b/blocksuite/affine/blocks/bookmark/src/adapters/markdown/preprocessor.ts
index 13dc5392f..5862b756a 100644
--- a/blocksuite/affine/blocks/bookmark/src/adapters/markdown/preprocessor.ts
+++ b/blocksuite/affine/blocks/bookmark/src/adapters/markdown/preprocessor.ts
@@ -23,12 +23,17 @@ type FootnoteDefinition = {
   content: FootNoteReferenceParams;
 };
 
-// Check if a URL is already encoded with encodeURIComponent
-function isEncoded(uri: string): boolean {
+/**
+ * Check if a URL is already encoded with encodeURIComponent to avoid markdown link parsing
+ * @example
+ * https://example.com/path%20with%20spaces should return false
+ * https://example.com/ should return false
+ * https%3A%2F%2Fexample.com%2F should return true
+ */
+function isFullyEncoded(uri: string): boolean {
   try {
-    // If decoding produces a different result than the original,
-    // then the URI contains encoded characters
-    return uri !== decodeURIComponent(uri);
+    // Should check if the components of the URI are fully encoded
+    return uri === encodeURIComponent(decodeURIComponent(uri));
   } catch {
     // If decoding fails, the URI contains invalid percent-encoding
     return true;
@@ -194,10 +199,10 @@ class FootnoteParser {
   // Process URLs in footnote content
   private processUrls(footnote: FootnoteDefinition): FootnoteDefinition {
     const content = footnote.content;
-    if (content.url && !isEncoded(content.url)) {
+    if (content.url && !isFullyEncoded(content.url)) {
       content.url = encodeURIComponent(content.url);
     }
-    if (content.favicon && !isEncoded(content.favicon)) {
+    if (content.favicon && !isFullyEncoded(content.favicon)) {
       content.favicon = encodeURIComponent(content.favicon);
     }
     return footnote;