diff --git a/src/mito2/src/read/batch_adapter.rs b/src/mito2/src/read/batch_adapter.rs
index 660d56c8ef..360f591658 100644
--- a/src/mito2/src/read/batch_adapter.rs
+++ b/src/mito2/src/read/batch_adapter.rs
@@ -682,7 +682,7 @@ mod tests {
         let rb = adapter.into_iter().next().unwrap().unwrap();
 
         let mapper = FlatProjectionMapper::new(&metadata, [0, 3].into_iter()).unwrap();
-        assert_eq!(rb.schema(), mapper.input_arrow_schema());
+        assert_eq!(rb.schema(), mapper.input_arrow_schema(false, None));
         // tag_0 + field_1 + ts + 3 internal columns.
         assert_eq!(6, rb.num_columns());
         assert_eq!(3, rb.num_rows());
diff --git a/src/mito2/src/read/flat_merge.rs b/src/mito2/src/read/flat_merge.rs
index 90df227ae9..1284daa5fa 100644
--- a/src/mito2/src/read/flat_merge.rs
+++ b/src/mito2/src/read/flat_merge.rs
@@ -18,6 +18,7 @@ use std::sync::Arc;
 use std::time::Instant;
 
 use async_stream::try_stream;
+use common_recordbatch::recordbatch::maybe_align_json_array_with_schema;
 use common_telemetry::debug;
 use datatypes::arrow::array::{Int64Array, UInt64Array};
 use datatypes::arrow::compute::interleave;
@@ -29,7 +30,7 @@ use futures::{Stream, TryStreamExt};
 use snafu::ResultExt;
 use store_api::storage::SequenceNumber;
 
-use crate::error::{ComputeArrowSnafu, Result};
+use crate::error::{ComputeArrowSnafu, RecordBatchSnafu, Result};
 use crate::memtable::BoxedRecordBatchIterator;
 use crate::metrics::READ_STAGE_ELAPSED;
 use crate::read::BoxedRecordBatchStream;
@@ -126,9 +127,12 @@ impl BatchBuilder {
                 let arrays: Vec<_> = self
                     .batches
                     .iter()
-                    .map(|(_, batch)| batch.column(column_idx).as_ref())
+                    .map(|(_, batch)| batch.column(column_idx).clone())
                     .collect();
-                interleave(&arrays, &self.indices).context(ComputeArrowSnafu)
+                let aligned = maybe_align_json_array_with_schema(&self.schema, arrays)
+                    .context(RecordBatchSnafu)?;
+                let aligned = aligned.iter().map(|x| x.as_ref()).collect::<Vec<_>>();
+                interleave(&aligned, &self.indices).context(ComputeArrowSnafu)
             })
             .collect::<Result<Vec<_>>>()?;
 
diff --git a/src/mito2/src/read/flat_projection.rs b/src/mito2/src/read/flat_projection.rs
index ff4fe498d4..8552c04f7d 100644
--- a/src/mito2/src/read/flat_projection.rs
+++ b/src/mito2/src/read/flat_projection.rs
@@ -39,7 +39,6 @@ use store_api::storage::ColumnId;
 use crate::cache::CacheStrategy;
 use crate::error::{InvalidRequestSnafu, RecordBatchSnafu, Result};
 use crate::read::projection::{read_column_ids_from_projection, repeated_vector_with_cache};
-use crate::read::scan_region::ScanInput;
 use crate::sst::parquet::flat_format::sst_column_id_indices;
 use crate::sst::parquet::format::FormatProjection;
 use crate::sst::{
@@ -223,20 +222,15 @@ impl FlatProjectionMapper {
         &self.batch_schema
     }
 
-    #[cfg(test)]
-    pub(crate) fn input_arrow_schema(&self) -> datatypes::arrow::datatypes::SchemaRef {
-        self.input_arrow_schema.clone()
-    }
-
     /// Returns the input arrow schema from sources.
     ///
     /// The merge reader can use this schema.
-    pub(crate) fn arrow_schema_by_compaction(
+    pub(crate) fn input_arrow_schema(
         &self,
-        scan_input: &ScanInput,
+        compaction: bool,
         json_concretized_schema: Option<ArrowSchemaRef>,
     ) -> datatypes::arrow::datatypes::SchemaRef {
-        if !scan_input.compaction {
+        if !compaction {
             self.input_arrow_schema.clone()
         } else {
             // For compaction, we need to build a different schema from encoding.
diff --git a/src/mito2/src/read/seq_scan.rs b/src/mito2/src/read/seq_scan.rs
index 1a78428564..60c523a732 100644
--- a/src/mito2/src/read/seq_scan.rs
+++ b/src/mito2/src/read/seq_scan.rs
@@ -216,7 +216,8 @@ impl SeqScan {
         }
 
         let mapper = stream_ctx.input.mapper.as_flat().unwrap();
-        let schema = mapper.arrow_schema_by_compaction(&stream_ctx.input, json_concretized_schema);
+        let schema =
+            mapper.input_arrow_schema(stream_ctx.input.compaction, json_concretized_schema);
 
         let metrics_reporter = part_metrics.map(|m| m.merge_metrics_reporter());
         let reader =