diff --git a/mittest/mtlenv/storage/blocksstable/test_index_tree.cpp b/mittest/mtlenv/storage/blocksstable/test_index_tree.cpp
index 00a345f5d0..8db60687f6 100644
--- a/mittest/mtlenv/storage/blocksstable/test_index_tree.cpp
+++ b/mittest/mtlenv/storage/blocksstable/test_index_tree.cpp
@@ -828,7 +828,22 @@ TEST_F(TestIndexTree, test_empty_index_tree)
   ASSERT_EQ(OB_SUCCESS, data_writer.open(data_desc.get_desc(), data_seq));
   // do not insert any data
   ASSERT_EQ(OB_SUCCESS, data_writer.close());
+  ASSERT_EQ(1, sstable_builder.roots_.count());
   ObSSTableMergeRes res;
+  ret = sstable_builder.close(res);
+  ASSERT_EQ(0, sstable_builder.roots_.count());
+  ASSERT_EQ(OB_SUCCESS, ret);
+  ASSERT_TRUE(res.root_desc_.is_empty());
+
+  // test rebuild macro blocks
+  ASSERT_EQ(OB_SUCCESS, data_writer.open(data_desc.get_desc(), data_seq));
+  // do not insert any data
+  ASSERT_EQ(OB_SUCCESS, data_writer.close());
+  ASSERT_EQ(1, sstable_builder.roots_.count());
+  ObSSTableIndexBuilder::ObMacroMetaIter macro_iter;
+  sstable_builder.init_meta_iter(macro_iter);
+  ASSERT_EQ(0, sstable_builder.roots_.count());
+
   ret = sstable_builder.close(res);
   ASSERT_EQ(OB_SUCCESS, ret);
   ASSERT_TRUE(res.root_desc_.is_empty());
diff --git a/src/storage/blocksstable/index_block/ob_index_block_builder.cpp b/src/storage/blocksstable/index_block/ob_index_block_builder.cpp
index 0f4a7746e8..73517cda15 100644
--- a/src/storage/blocksstable/index_block/ob_index_block_builder.cpp
+++ b/src/storage/blocksstable/index_block/ob_index_block_builder.cpp
@@ -689,7 +689,10 @@ int ObSSTableIndexBuilder::init_meta_iter(ObMacroMetaIter &iter)
   if (IS_NOT_INIT) {
     ret = OB_NOT_INIT;
     STORAGE_LOG(WARN, "invalid sstable builder", K(ret), K_(is_inited));
-  } else if (FALSE_IT(sort_roots())) {
+  } else if (OB_FAIL(trim_empty_roots())) {
+    STORAGE_LOG(WARN, "fail to trim empty roots", K(ret));
+  } else if (OB_FAIL(sort_roots())) {
+    STORAGE_LOG(WARN, "fail to sort roots", K(ret));
   } else if (OB_FAIL(iter.init(roots_, index_store_desc_.get_desc().is_cg()))) {
     STORAGE_LOG(WARN, "fail to init iter", K(ret));
   }