diff --git a/src/mito2/src/read/read_columns.rs b/src/mito2/src/read/read_columns.rs
index ae5876237b..2178fa2538 100644
--- a/src/mito2/src/read/read_columns.rs
+++ b/src/mito2/src/read/read_columns.rs
@@ -170,7 +170,7 @@ fn normalize_nested_paths(nested_paths: Vec<NestedPath>) -> Vec<NestedPath> {
     normalized
 }
 
-fn merge_nested_paths(merged: &mut Vec<NestedPath>, incoming: Vec<NestedPath>) {
+pub(crate) fn merge_nested_paths(merged: &mut Vec<NestedPath>, incoming: Vec<NestedPath>) {
     for path in incoming {
         if merged
             .iter()
diff --git a/src/mito2/src/read/scan_region.rs b/src/mito2/src/read/scan_region.rs
index 8894e970d2..3fe1aad6d7 100644
--- a/src/mito2/src/read/scan_region.rs
+++ b/src/mito2/src/read/scan_region.rs
@@ -61,7 +61,8 @@ use crate::read::flat_projection::FlatProjectionMapper;
 use crate::read::range::{FileRangeBuilder, MemRangeBuilder, RangeMeta, RowGroupIndex};
 use crate::read::range_cache::{ScanRequestFingerprint, implied_time_range_from_exprs};
 use crate::read::read_columns::{
-    ReadColumns, merge, read_columns_from_predicate, read_columns_from_projection,
+    ReadColumns, merge, merge_nested_paths, read_columns_from_predicate,
+    read_columns_from_projection,
 };
 use crate::read::seq_scan::SeqScan;
 use crate::read::series_scan::SeriesScan;
@@ -1340,7 +1341,7 @@ fn fill_json_nested_paths_from_hint(
         let mut paths = Vec::new();
         let mut current = vec![column_name.clone()];
         collect_json_nested_paths(json_type, &mut current, &mut paths);
-        read_column.nested_paths = paths;
+        merge_nested_paths(&mut read_column.nested_paths, paths)
     }
 }
 
diff --git a/src/mito2/src/sst/parquet/flat_format.rs b/src/mito2/src/sst/parquet/flat_format.rs
index 53e16f86eb..39d8691a13 100644
--- a/src/mito2/src/sst/parquet/flat_format.rs
+++ b/src/mito2/src/sst/parquet/flat_format.rs
@@ -452,9 +452,22 @@ where
         .fields
         .into_iter()
         .zip(nested_paths)
-        .map(|(field, nested_paths)| {
-            let nested_paths = nested_paths.iter().map(Vec::as_slice).collect::<Vec<_>>();
-            prune_field_by_nested_paths(field, &nested_paths)
+        .map(|(field, paths)| {
+            if matches!(field.data_type(), ArrowDataType::Struct(_)) && !paths.is_empty() {
+                let child_paths = paths
+                    .iter()
+                    .map(|path| {
+                        if path.first().is_some_and(|root| root == field.name()) {
+                            &path[1..]
+                        } else {
+                            path
+                        }
+                    })
+                    .collect::<Vec<_>>();
+                prune_field_by_nested_paths(field, &child_paths)
+            } else {
+                field.clone()
+            }
         })
         .collect::<Vec<_>>();
     schema.fields = fields.into()
@@ -465,32 +478,14 @@ fn prune_field_by_nested_paths(field: &FieldRef, nested_paths: &[&[String]]) ->
         return field.clone();
     };
 
-    if nested_paths.is_empty() {
-        return field.clone();
-    }
-
-    let child_paths = nested_paths
-        .iter()
-        .map(|path| {
-            if path.first().is_some_and(|root| root == field.name()) {
-                &path[1..]
-            } else {
-                *path
-            }
-        })
-        .collect::<Vec<_>>();
-    if child_paths.iter().any(|path| path.is_empty()) {
-        return field.clone();
-    }
-
     let pruned_fields = fields
         .iter()
         .filter_map(|field| {
-            let child_paths = child_paths
+            let child_paths = nested_paths
                 .iter()
                 .filter_map(|path| {
                     path.first()
-                        .is_some_and(|name| name.as_str() == field.name().as_str())
+                        .is_some_and(|name| name == field.name())
                         .then_some(&path[1..])
                 })
                 .collect::<Vec<_>>();
diff --git a/src/mito2/src/test_util.rs b/src/mito2/src/test_util.rs
index ba321f4383..45f2e9c905 100644
--- a/src/mito2/src/test_util.rs
+++ b/src/mito2/src/test_util.rs
@@ -905,12 +905,16 @@ impl CreateRequestBuilder {
             column_id += 1;
         }
         for i in 0..self.field_num {
+            let mut column_schema =
+                ColumnSchema::new(format!("field_{i}"), self.field_datatype.clone(), nullable);
+            if self.field_datatype.is_json() {
+                column_schema.mut_metadata().insert(
+                    EXTENSION_TYPE_NAME_KEY.to_string(),
+                    JsonExtensionType::NAME.to_string(),
+                );
+            }
             column_metadatas.push(ColumnMetadata {
-                column_schema: ColumnSchema::new(
-                    format!("field_{i}"),
-                    self.field_datatype.clone(),
-                    nullable,
-                ),
+                column_schema,
                 semantic_type: SemanticType::Field,
                 column_id,
             });