diff --git a/dbms/src/Storages/Page/V3/PageDirectory.cpp b/dbms/src/Storages/Page/V3/PageDirectory.cpp
index afa8fcf1a6d..8f2b867c929 100644
--- a/dbms/src/Storages/Page/V3/PageDirectory.cpp
+++ b/dbms/src/Storages/Page/V3/PageDirectory.cpp
@@ -108,37 +108,12 @@ void PageDirectory::apply(PageEntriesEdit && edit)
     std::unique_lock write_lock(table_rw_mutex); // TODO: It is totally serialized, make it a pipeline
     UInt64 last_sequence = sequence.load();
 
-    // stage 1, get the entry to be ref
     auto snap = createSnapshot();
-    for (auto & r : edit.getRecords())
-    {
-        // Set the version of inserted entries
-        r.version = PageVersionType(last_sequence + 1);
-
-        if (r.type != WriteBatch::WriteType::REF)
-        {
-            continue;
-        }
-        auto iter = mvcc_table_directory.find(r.ori_page_id);
-        if (iter == mvcc_table_directory.end())
-        {
-            throw Exception(fmt::format("Trying to add ref from {} to non-exist {} with sequence={}", r.page_id, r.ori_page_id, last_sequence + 1), ErrorCodes::LOGICAL_ERROR);
-        }
-        if (auto entry = iter->second->getEntry(last_sequence); entry)
-        {
-            // copy the entry to be ref
-            r.entry = *entry;
-        }
-        else
-        {
-            throw Exception(fmt::format("Trying to add ref from {} to non-exist {} with sequence={}", r.page_id, r.ori_page_id, last_sequence + 1), ErrorCodes::LOGICAL_ERROR);
-        }
-    }
 
-    // stage 2, persisted the changes to WAL
+    // stage 1, persisted the changes to WAL
     // wal.apply(edit);
 
-    // stage 3, create entry version list for pageId. nothing need to be rollback
+    // stage 2, create entry version list for pageId. nothing need to be rollback
     std::unordered_map<PageId, std::pair<PageLock, int>> updating_locks;
     std::vector<VersionedPageEntriesPtr> updating_pages;
     updating_pages.reserve(edit.size());
@@ -163,7 +138,7 @@ void PageDirectory::apply(PageEntriesEdit && edit)
         updating_pages.emplace_back(iter->second);
     }
 
-    // stage 4, there are no rollback since we already persist `edit` to WAL, just ignore error if any
+    // stage 3, there are no rollback since we already persist `edit` to WAL, just ignore error if any
     const auto & records = edit.getRecords();
     for (size_t idx = 0; idx < records.size(); ++idx)
     {
@@ -173,11 +148,31 @@ void PageDirectory::apply(PageEntriesEdit && edit)
         case WriteBatch::WriteType::PUT:
             [[fallthrough]];
         case WriteBatch::WriteType::UPSERT:
-            [[fallthrough]];
+            updating_pages[idx]->createNewVersion(last_sequence + 1, r.entry);
+            break;
         case WriteBatch::WriteType::REF:
         {
-            // Put/upsert/ref all should append a new version for this page
-            updating_pages[idx]->createNewVersion(last_sequence + 1, r.entry);
+            // We can't handle `REF` before other writes, because `PUT` and `REF`
+            // maybe in the same WriteBatch.
+            // Also we can't throw an exception if we can't find the origin page_id,
+            // because WAL have already applied the change and there is no
+            // mechanism to roll back changes in the WAL.
+            auto iter = mvcc_table_directory.find(r.ori_page_id);
+            if (iter == mvcc_table_directory.end())
+            {
+                LOG_FMT_WARNING(log, "Trying to add ref from {} to non-exist {} with sequence={}", r.page_id, r.ori_page_id, last_sequence + 1);
+                break;
+            }
+
+            if (auto entry = iter->second->getEntry(last_sequence); entry)
+            {
+                // copy the entry to be ref
+                updating_pages[idx]->createNewVersion(last_sequence + 1, *entry);
+            }
+            else
+            {
+                LOG_FMT_WARNING(log, "Trying to add ref from {} to non-exist {} with sequence={}", r.page_id, r.ori_page_id, last_sequence + 1);
+            }
             break;
         }
         case WriteBatch::WriteType::DEL:
diff --git a/dbms/src/Storages/Page/V3/PageEntriesEdit.h b/dbms/src/Storages/Page/V3/PageEntriesEdit.h
index 0ef63a29e0b..e1d601a634d 100644
--- a/dbms/src/Storages/Page/V3/PageEntriesEdit.h
+++ b/dbms/src/Storages/Page/V3/PageEntriesEdit.h
@@ -96,7 +96,6 @@ class PageEntriesEdit
         PageId page_id;
         PageId ori_page_id;
         PageEntryV3 entry;
-        PageVersionType version;
     };
     using EditRecords = std::vector<EditRecord>;
 
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 d039adcdf23..94a8099bcdc 100644
--- a/dbms/src/Storages/Page/V3/tests/gtest_page_directory.cpp
+++ b/dbms/src/Storages/Page/V3/tests/gtest_page_directory.cpp
@@ -608,6 +608,7 @@ try
 {
     PageEntryV3 entry1{.file_id = 1, .size = 1024, .offset = 0x123, .checksum = 0x4567};
     PageEntryV3 entry2{.file_id = 2, .size = 1024, .offset = 0x123, .checksum = 0x4567};
+    PageEntryV3 entry3{.file_id = 3, .size = 1024, .offset = 0x123, .checksum = 0x4567};
     {
         PageEntriesEdit edit;
         edit.put(1, entry1);
@@ -615,14 +616,17 @@ try
         dir.apply(std::move(edit));
     }
 
-    { // Ref 3-> 999
+    { // Ref 4-> 999
         PageEntriesEdit edit;
-        edit.ref(3, 999);
-        ASSERT_THROW({ dir.apply(std::move(edit)); }, DB::Exception);
+        edit.put(3, entry3);
+        edit.ref(4, 999);
+        dir.apply(std::move(edit));
     }
     auto snap1 = dir.createSnapshot();
+    EXPECT_ENTRY_EQ(entry1, dir, 1, snap1);
     EXPECT_ENTRY_EQ(entry2, dir, 2, snap1);
-    EXPECT_ENTRY_NOT_EXIST(dir, 3, snap1);
+    EXPECT_ENTRY_EQ(entry3, dir, 3, snap1);
+    EXPECT_ENTRY_NOT_EXIST(dir, 4, snap1);
 
     // TODO: restore, invalid ref page is filtered
 }