diff --git a/dbms/src/Storages/Page/V3/PageDirectoryFactory.cpp b/dbms/src/Storages/Page/V3/PageDirectoryFactory.cpp
index 9d20e0a64ab..149807eab38 100644
--- a/dbms/src/Storages/Page/V3/PageDirectoryFactory.cpp
+++ b/dbms/src/Storages/Page/V3/PageDirectoryFactory.cpp
@@ -42,6 +42,22 @@ PageDirectoryPtr PageDirectoryFactory::create(String storage_name, FileProviderP
     dir->gcInMemEntries();
     LOG_FMT_INFO(DB::Logger::get("PageDirectoryFactory"), "PageDirectory restored [max_page_id={}] [max_applied_ver={}]", dir->getMaxId(), dir->sequence);
 
+    // MVCC gc must do twice when restore
+    // Because the first time call MVCC GC may not clean the deleted entries if being reference.
+    // But it will clean up the deleted reference.
+    // ex.
+    //  P 1
+    //  R 2 -> 1
+    //  D 1
+    //  D 2
+    // First time call gcInMemEntries():
+    //  - P 1 entry 0 being_ref_count is not zero, won't be cleaned.
+    //  - R 2 entry 0 being_ref_count is zero, deref the P 1, make it being_ref_count is 0. Also R2 will be clean up.
+    //
+    // Second time call gcInMemEntries():
+    //  - P 1 being_ref_count is 0, it will be clean.
+    dir->gcInMemEntries();
+
     if (blob_stats)
     {
         // After all entries restored to `mvcc_table_directory`, only apply
diff --git a/dbms/src/Storages/Page/V3/tests/gtest_page_directory.cpp b/dbms/src/Storages/Page/V3/tests/gtest_page_directory.cpp
index 151b3b50657..e98c68fd9c3 100644
--- a/dbms/src/Storages/Page/V3/tests/gtest_page_directory.cpp
+++ b/dbms/src/Storages/Page/V3/tests/gtest_page_directory.cpp
@@ -2214,6 +2214,35 @@ try
 }
 CATCH
 
+TEST_F(PageDirectoryGCTest, testGCTwice)
+try
+{
+    PageEntryV3 entry_50_1{.file_id = 1, .size = 7890, .tag = 0, .offset = 0x123, .checksum = 0x4567};
+    PageEntryV3 entry_50_2{.file_id = 2, .size = 7890, .tag = 0, .offset = 0x123, .checksum = 0x4567};
+
+    auto restore_from_edit = [](const PageEntriesEdit & edit) {
+        auto ctx = ::DB::tests::TiFlashTestEnv::getContext();
+        auto provider = ctx.getFileProvider();
+        auto path = getTemporaryPath();
+        PSDiskDelegatorPtr delegator = std::make_shared<DB::tests::MockDiskDelegatorSingle>(path);
+        PageDirectoryFactory factory;
+        auto d = factory.createFromEdit(getCurrentTestName(), provider, delegator, edit);
+        return d;
+    };
+
+    {
+        PageEntriesEdit edit;
+        edit.put(50, entry_50_1);
+        edit.put(50, entry_50_2);
+        edit.ref(51, 50);
+        edit.del(50);
+        edit.del(51);
+        auto page_ids = restore_from_edit(edit)->getAllPageIds();
+        ASSERT_EQ(page_ids.size(), 0);
+    }
+}
+CATCH
+
 #undef INSERT_ENTRY_TO
 #undef INSERT_ENTRY
 #undef INSERT_ENTRY_ACQ_SNAP
diff --git a/dbms/src/Storages/Page/V3/tests/gtest_page_storage.cpp b/dbms/src/Storages/Page/V3/tests/gtest_page_storage.cpp
index 498fd4124e5..049d839afb9 100644
--- a/dbms/src/Storages/Page/V3/tests/gtest_page_storage.cpp
+++ b/dbms/src/Storages/Page/V3/tests/gtest_page_storage.cpp
@@ -1329,6 +1329,7 @@ try
 }
 CATCH
 
+
 TEST_F(PageStorageTest, GetMaxId)
 try
 {
@@ -1380,5 +1381,33 @@ try
 }
 CATCH
 
+TEST_F(PageStorageTest, testGCTwice)
+try
+{
+    // Make it in log_1_0
+    {
+        WriteBatch batch;
+        batch.putExternal(1, 0);
+        page_storage->write(std::move(batch));
+    }
+
+    page_storage = reopenWithConfig(config);
+
+    // Make it in log_2_0
+    {
+        WriteBatch batch;
+        batch.putExternal(1, 0);
+        batch.putRefPage(2, 1);
+        batch.delPage(1);
+        batch.delPage(2);
+        page_storage->write(std::move(batch));
+    }
+    page_storage = reopenWithConfig(config);
+
+    auto alive_ids = page_storage->getAliveExternalPageIds(TEST_NAMESPACE_ID);
+    ASSERT_EQ(alive_ids.size(), 0);
+}
+CATCH
+
 } // namespace PS::V3::tests
 } // namespace DB