diff --git a/src/Storages/MergeTree/MergeTreeData.cpp b/src/Storages/MergeTree/MergeTreeData.cpp
index 3e9926239672..58b5efae215d 100644
--- a/src/Storages/MergeTree/MergeTreeData.cpp
+++ b/src/Storages/MergeTree/MergeTreeData.cpp
@@ -4461,6 +4461,14 @@ MergeTreeDataPartFormat MergeTreeData::choosePartFormat(size_t bytes_uncompresse
     using PartType = MergeTreeDataPartType;
     using PartStorageType = MergeTreeDataPartStorageType;
 
+    /// Deprecated Object type doesn't work correctly with compact parts
+    /// when write_marks_for_substreams_in_compact_parts is disabled,
+    /// because the compact reader cannot properly handle missing substreams
+    /// in complex nested Tuple structures that Object converts to.
+    /// Force wide parts for such tables to avoid deserialization crashes.
+    if (hasDynamicSubcolumnsDeprecated(getInMemoryMetadataPtr()->getColumns()))
+        return {PartType::Wide, PartStorageType::Full};
+
     String out_reason;
     const auto settings = getSettings();
     if (!canUsePolymorphicParts(*settings, out_reason))
diff --git a/tests/queries/0_stateless/03779_object_in_compact_mergetree_parts.reference b/tests/queries/0_stateless/03779_object_in_compact_mergetree_parts.reference
new file mode 100644
index 000000000000..53742b87fafc
--- /dev/null
+++ b/tests/queries/0_stateless/03779_object_in_compact_mergetree_parts.reference
@@ -0,0 +1,4 @@
+1	[['aaa','ccc']]	[['bbb','']]	[[0,0]]	['']
+2	[['','']]	[['ddd','']]	[[10,20]]	['foo']
+1	[['aaa','ccc']]	[['bbb','']]	[[0,0]]	['']
+2	[['','']]	[['ddd','']]	[[10,20]]	['foo']
diff --git a/tests/queries/0_stateless/03779_object_in_compact_mergetree_parts.sql b/tests/queries/0_stateless/03779_object_in_compact_mergetree_parts.sql
new file mode 100644
index 000000000000..06ab06abca96
--- /dev/null
+++ b/tests/queries/0_stateless/03779_object_in_compact_mergetree_parts.sql
@@ -0,0 +1,32 @@
+SET allow_experimental_object_type = 1;
+
+-- Test with the setting being disabled
+DROP TABLE IF EXISTS t_json_complex;
+CREATE TABLE t_json_complex (id UInt32, arr Array(Object('json')))
+ENGINE = MergeTree ORDER BY id
+SETTINGS write_marks_for_substreams_in_compact_parts=0;
+
+-- Insert data with nested arrays inside JSON objects
+INSERT INTO t_json_complex FORMAT JSONEachRow {"id": 1, "arr": [{"k1": [{"k2": "aaa", "k3": "bbb"}, {"k2": "ccc"}]}]}
+
+INSERT INTO t_json_complex FORMAT JSONEachRow {"id": 2, "arr": [{"k1": [{"k3": "ddd", "k4": 10}, {"k4": 20}], "k5": {"k6": "foo"}}]}
+
+-- This query used to crash the server
+SELECT id, arr.k1.k2, arr.k1.k3, arr.k1.k4, arr.k5.k6 FROM t_json_complex ORDER BY id;
+DROP TABLE t_json_complex;
+
+-- Now test with the setting explicitly enabled
+DROP TABLE IF EXISTS t_json_complex_compact_parts;
+CREATE TABLE t_json_complex_compact_parts (id UInt32, arr Array(Object('json')))
+ENGINE = MergeTree ORDER BY id
+SETTINGS write_marks_for_substreams_in_compact_parts=1;
+
+-- Insert data with nested arrays inside JSON objects
+INSERT INTO t_json_complex_compact_parts FORMAT JSONEachRow {"id": 1, "arr": [{"k1": [{"k2": "aaa", "k3": "bbb"}, {"k2": "ccc"}]}]}
+
+INSERT INTO t_json_complex_compact_parts FORMAT JSONEachRow {"id": 2, "arr": [{"k1": [{"k3": "ddd", "k4": 10}, {"k4": 20}], "k5": {"k6": "foo"}}]}
+
+-- This query used to crash the server
+SELECT id, arr.k1.k2, arr.k1.k3, arr.k1.k4, arr.k5.k6 FROM t_json_complex_compact_parts ORDER BY id;
+DROP TABLE t_json_complex_compact_parts;
+