diff --git a/src/mito2/src/sst/parquet/flat_format.rs b/src/mito2/src/sst/parquet/flat_format.rs
index 5e8debe3c6..dda150485e 100644
--- a/src/mito2/src/sst/parquet/flat_format.rs
+++ b/src/mito2/src/sst/parquet/flat_format.rs
@@ -140,6 +140,8 @@ pub struct FlatReadFormat {
 
 impl FlatReadFormat {
     /// Creates a helper with existing `metadata` and `column_ids` to read.
+    ///
+    /// If `skip_auto_convert` is true, skips auto conversion of format when the encoding is sparse encoding.
     pub fn new(
         metadata: RegionMetadataRef,
         column_ids: impl Iterator<Item = ColumnId>,
@@ -154,11 +156,18 @@ impl FlatReadFormat {
 
         let parquet_adapter = if is_legacy {
             // Safety: is_legacy_format() ensures primary_key is not empty.
-            ParquetAdapter::PrimaryKeyToFlat(ParquetPrimaryKeyToFlat::new(
-                metadata,
-                column_ids,
-                skip_auto_convert,
-            ))
+            if metadata.primary_key_encoding == PrimaryKeyEncoding::Sparse {
+                // Only skip auto convert when the primary key encoding is sparse.
+                ParquetAdapter::PrimaryKeyToFlat(ParquetPrimaryKeyToFlat::new(
+                    metadata,
+                    column_ids,
+                    skip_auto_convert,
+                ))
+            } else {
+                ParquetAdapter::PrimaryKeyToFlat(ParquetPrimaryKeyToFlat::new(
+                    metadata, column_ids, false,
+                ))
+            }
         } else {
             ParquetAdapter::Flat(ParquetFlat::new(metadata, column_ids))
         };
@@ -370,6 +379,12 @@ impl ParquetPrimaryKeyToFlat {
         column_ids: impl Iterator<Item = ColumnId>,
         skip_auto_convert: bool,
     ) -> ParquetPrimaryKeyToFlat {
+        assert!(if skip_auto_convert {
+            metadata.primary_key_encoding == PrimaryKeyEncoding::Sparse
+        } else {
+            true
+        });
+
         let column_ids: Vec<_> = column_ids.collect();
 
         // Creates a map to lookup index based on the new format.
diff --git a/src/mito2/src/sst/parquet/format.rs b/src/mito2/src/sst/parquet/format.rs
index 48eca5879a..4297071e4d 100644
--- a/src/mito2/src/sst/parquet/format.rs
+++ b/src/mito2/src/sst/parquet/format.rs
@@ -1740,7 +1740,7 @@ mod tests {
             .collect();
         let format = FlatReadFormat::new(
             metadata.clone(),
-            column_ids.into_iter(),
+            column_ids.clone().into_iter(),
             None,
             "test",
             false,
@@ -1797,7 +1797,7 @@ mod tests {
         let record_batch = RecordBatch::try_new(old_schema, columns).unwrap();
 
         // Test conversion with sparse encoding
-        let result = format.convert_batch(record_batch, None).unwrap();
+        let result = format.convert_batch(record_batch.clone(), None).unwrap();
 
         // Construct expected RecordBatch in flat format with decoded primary key columns
         let tag0_array = Arc::new(DictionaryArray::new(
@@ -1826,5 +1826,12 @@ mod tests {
 
         // Compare the actual result with the expected record batch
         assert_eq!(expected_record_batch, result);
+
+        let format =
+            FlatReadFormat::new(metadata.clone(), column_ids.into_iter(), None, "test", true)
+                .unwrap();
+        // Test conversion with sparse encoding and skip convert.
+        let result = format.convert_batch(record_batch.clone(), None).unwrap();
+        assert_eq!(record_batch, result);
     }
 }