diff --git a/src/meta/src/hummock/compaction/picker/base_level_compaction_picker.rs b/src/meta/src/hummock/compaction/picker/base_level_compaction_picker.rs
index 548d2201bd46c..ed375041aad46 100644
--- a/src/meta/src/hummock/compaction/picker/base_level_compaction_picker.rs
+++ b/src/meta/src/hummock/compaction/picker/base_level_compaction_picker.rs
@@ -134,11 +134,6 @@ impl LevelCompactionPicker {
         level_handlers: &[LevelHandler],
         stats: &mut LocalPickerStatistic,
     ) -> Option<CompactionInput> {
-        if l0.sub_levels.len() < 1 || l0.sub_levels[0].vnode_partition_count < vnode_partition_count
-        {
-            return None;
-        }
-
         let overlap_strategy = create_overlap_strategy(self.config.compaction_mode());
         let min_compaction_bytes = self.config.sub_level_max_compaction_bytes;
         let non_overlap_sub_level_picker = NonOverlapSubLevelPicker::new(
diff --git a/src/meta/src/hummock/compaction/selector/level_selector.rs b/src/meta/src/hummock/compaction/selector/level_selector.rs
index a43cdbf5e15fa..ae8379ad1ec9c 100644
--- a/src/meta/src/hummock/compaction/selector/level_selector.rs
+++ b/src/meta/src/hummock/compaction/selector/level_selector.rs
@@ -224,7 +224,18 @@ impl DynamicLevelSelectorCore {
             // range at each level, so the number of levels is the most important factor affecting
             // the read performance. At the same time, the size factor is also added to the score
             // calculation rule to avoid unbalanced compact task due to large size.
-            let total_size = levels.l0.as_ref().unwrap().total_file_size
+            let total_size = levels
+                .l0
+                .as_ref()
+                .unwrap()
+                .sub_levels
+                .iter()
+                .filter(|level| {
+                    level.vnode_partition_count == levels.vnode_partition_count
+                        && level.level_type() == LevelType::Nonoverlapping
+                })
+                .map(|level| level.total_file_size)
+                .sum::<u64>()
                 - handlers[0].get_pending_output_file_size(ctx.base_level as u32);
             let base_level_size = levels.get_level(ctx.base_level).total_file_size;
             let base_level_sst_count = levels.get_level(ctx.base_level).table_infos.len() as u64;