diff --git a/apps/readest-app/src/__tests__/fixtures/data/repro-3688.epub b/apps/readest-app/src/__tests__/fixtures/data/repro-3688.epub
new file mode 100644
index 00000000..bc44d41b
Binary files /dev/null and b/apps/readest-app/src/__tests__/fixtures/data/repro-3688.epub differ
diff --git a/apps/readest-app/src/__tests__/utils/toc-cfi-mapping.test.ts b/apps/readest-app/src/__tests__/utils/toc-cfi-mapping.test.ts
new file mode 100644
index 00000000..e8901c81
--- /dev/null
+++ b/apps/readest-app/src/__tests__/utils/toc-cfi-mapping.test.ts
@@ -0,0 +1,107 @@
+import { describe, it, expect, beforeAll, vi } from 'vitest';
+import { readFileSync } from 'fs';
+import { resolve } from 'path';
+import { DocumentLoader } from '@/libs/document';
+import type { BookDoc, TOCItem } from '@/libs/document';
+import { updateToc, findTocItemBS } from '@/utils/toc';
+
+// Polyfill CSS.escape for jsdom
+if (typeof globalThis['CSS'] === 'undefined') {
+  (globalThis as Record<string, unknown>)['CSS'] = {
+    escape: (s: string) => s.replace(/([^\w-])/g, '\\$1'),
+  };
+}
+
+// Register a stub paginator custom element so View.open() doesn't fail in jsdom
+if (!customElements.get('foliate-paginator')) {
+  customElements.define(
+    'foliate-paginator',
+    class extends HTMLElement {
+      override setAttribute() {}
+      override addEventListener() {}
+      open() {}
+    },
+  );
+}
+
+// Mock the paginator module import so View doesn't try to load the real one
+vi.mock('foliate-js/paginator.js', () => ({}));
+
+/**
+ * Regression test for https://github.com/readest/readest/issues/3688
+ *
+ * When TOC entries use fragment-suffixed hrefs (e.g. ch01.xhtml#ch01),
+ * all annotations were incorrectly grouped under the last chapter.
+ * This happened because section subitems created during EPUB init had
+ * cfi: undefined, and the sectionsMap lookup found these subitems
+ * instead of the parent sections with valid CFIs.
+ */
+describe('TOC-to-CFI mapping with fragment hrefs (#3688)', () => {
+  let book: BookDoc;
+
+  beforeAll(async () => {
+    const epubPath = resolve(__dirname, '../fixtures/data/repro-3688.epub');
+    const buffer = readFileSync(epubPath);
+    const file = new File([buffer], 'repro-3688.epub', {
+      type: 'application/epub+zip',
+    });
+    const loader = new DocumentLoader(file);
+    const result = await loader.open();
+    book = result.book;
+    await updateToc(book, false, 'none');
+  }, 30000);
+
+  it('should assign valid CFIs to all TOC items', () => {
+    const toc = book.toc ?? [];
+    expect(toc.length).toBeGreaterThan(0);
+
+    const collectItems = (items: TOCItem[]): TOCItem[] =>
+      items.flatMap((item) => [item, ...(item.subitems ? collectItems(item.subitems) : [])]);
+
+    const allItems = collectItems(toc);
+    const itemsWithHref = allItems.filter((item) => item.href);
+    expect(itemsWithHref.length).toBeGreaterThan(1);
+
+    // Every TOC item with an href should have a valid (non-empty) CFI
+    for (const item of itemsWithHref) {
+      expect(
+        item.cfi,
+        `TOC item "${item.label}" (href: ${item.href}) should have a valid CFI`,
+      ).toBeTruthy();
+    }
+  });
+
+  it('should map CFIs from different sections to different TOC items', () => {
+    const toc = book.toc ?? [];
+    const sections = book.sections ?? [];
+    expect(sections.length).toBeGreaterThan(1);
+
+    const linearSections = sections.filter((s) => s.linear !== 'no' && s.cfi);
+    expect(linearSections.length).toBeGreaterThan(2);
+
+    const firstSection = linearSections[0]!;
+    const lastSection = linearSections[linearSections.length - 1]!;
+
+    const firstTocItem = findTocItemBS(toc, firstSection.cfi);
+    const lastTocItem = findTocItemBS(toc, lastSection.cfi);
+
+    expect(firstTocItem).not.toBeNull();
+    expect(lastTocItem).not.toBeNull();
+
+    // Annotations from different sections must NOT all map to the same chapter
+    expect(firstTocItem!.label).toBe('Chapter One');
+    expect(lastTocItem!.label).toBe('Chapter Three');
+  });
+
+  it('should map a mid-book CFI to a mid-book TOC item, not the last one', () => {
+    const toc = book.toc ?? [];
+    const sections = book.sections ?? [];
+    const linearSections = sections.filter((s) => s.linear !== 'no' && s.cfi);
+
+    const midSection = linearSections[1]!;
+    const midTocItem = findTocItemBS(toc, midSection.cfi);
+
+    expect(midTocItem).not.toBeNull();
+    expect(midTocItem!.label).toBe('Chapter Two');
+  });
+});
diff --git a/apps/readest-app/src/utils/toc.ts b/apps/readest-app/src/utils/toc.ts
index 00886be5..84108f88 100644
--- a/apps/readest-app/src/utils/toc.ts
+++ b/apps/readest-app/src/utils/toc.ts
@@ -193,7 +193,9 @@ const updateTocLocation = (
     item.id ??= index++;
     if (item.href) {
       const id = bookDoc.splitTOCHref(item.href)[0]!;
-      const section = sectionsMap[item.href] || sectionsMap[id];
+      const exactMatch = sectionsMap[item.href];
+      const baseMatch = sectionsMap[id];
+      const section = (exactMatch?.cfi ? exactMatch : null) || baseMatch || exactMatch;
       if (section) {
         item.cfi = section.cfi;
         if (