diff --git a/be/src/olap/rowset/segment_v2/vertical_segment_writer.cpp b/be/src/olap/rowset/segment_v2/vertical_segment_writer.cpp
index 80c8f78e093b43..7e9a1cdf1e9659 100644
--- a/be/src/olap/rowset/segment_v2/vertical_segment_writer.cpp
+++ b/be/src/olap/rowset/segment_v2/vertical_segment_writer.cpp
@@ -528,8 +528,6 @@ Status VerticalSegmentWriter::_append_block_with_partial_content(RowsInBlock& da
     for (auto i : including_cids) {
         full_block.replace_by_position(i, data.block->get_by_position(input_id++).column);
     }
-    RETURN_IF_ERROR(_olap_data_convertor->set_source_content_with_specifid_columns(
-            &full_block, data.row_pos, data.num_rows, including_cids));
 
     bool have_input_seq_column = false;
     // write including columns
@@ -537,6 +535,8 @@ Status VerticalSegmentWriter::_append_block_with_partial_content(RowsInBlock& da
     vectorized::IOlapColumnDataAccessor* seq_column = nullptr;
     uint32_t segment_start_pos = 0;
     for (auto cid : including_cids) {
+        RETURN_IF_ERROR(_olap_data_convertor->set_source_content_with_specifid_columns(
+                &full_block, data.row_pos, data.num_rows, std::vector<uint32_t> {cid}));
         // here we get segment column row num before append data.
         segment_start_pos = cast_set<uint32_t>(_column_writers[cid]->get_next_rowid());
         // olap data convertor alway start from id = 0
@@ -554,6 +554,15 @@ Status VerticalSegmentWriter::_append_block_with_partial_content(RowsInBlock& da
         RETURN_IF_ERROR(_column_writers[cid]->append(column->get_nullmap(), column->get_data(),
                                                      data.num_rows));
         RETURN_IF_ERROR(_finalize_column_writer_and_update_meta(cid));
+        // Don't clear source content for key columns and sequence column here,
+        // as they will be used later in _full_encode_keys() and _generate_primary_key_index().
+        // They will be cleared at the end of this method.
+        bool is_key_column = (cid < _num_sort_key_columns);
+        bool is_seq_column = (_tablet_schema->has_sequence_col() &&
+                              cid == _tablet_schema->sequence_col_idx() && have_input_seq_column);
+        if (!is_key_column && !is_seq_column) {
+            _olap_data_convertor->clear_source_content(cid);
+        }
     }
 
     bool has_default_or_nullable = false;
@@ -629,9 +638,9 @@ Status VerticalSegmentWriter::_append_block_with_partial_content(RowsInBlock& da
 
     // convert missing columns and send to column writer
     const auto& missing_cids = _opts.rowset_ctx->partial_update_info->missing_cids;
-    RETURN_IF_ERROR(_olap_data_convertor->set_source_content_with_specifid_columns(
-            &full_block, data.row_pos, data.num_rows, missing_cids));
     for (auto cid : missing_cids) {
+        RETURN_IF_ERROR(_olap_data_convertor->set_source_content_with_specifid_columns(
+                &full_block, data.row_pos, data.num_rows, std::vector<uint32_t> {cid}));
         auto [status, column] = _olap_data_convertor->convert_column_data(cid);
         if (!status.ok()) {
             return status;
@@ -644,6 +653,13 @@ Status VerticalSegmentWriter::_append_block_with_partial_content(RowsInBlock& da
         RETURN_IF_ERROR(_column_writers[cid]->append(column->get_nullmap(), column->get_data(),
                                                      data.num_rows));
         RETURN_IF_ERROR(_finalize_column_writer_and_update_meta(cid));
+        // Don't clear source content for sequence column here if it will be used later
+        // in _generate_primary_key_index(). It will be cleared at the end of this method.
+        bool is_seq_column = (_tablet_schema->has_sequence_col() && !have_input_seq_column &&
+                              cid == _tablet_schema->sequence_col_idx());
+        if (!is_seq_column) {
+            _olap_data_convertor->clear_source_content(cid);
+        }
     }
 
     _num_rows_updated += stats.num_rows_updated;