A memory system includes: a memory device including map memory blocks and data memory blocks; and a controller suitable to: detect, as victim memory blocks, map memory blocks each having an erase count less than or equal to an average erase count of the data memory blocks when an average erase count of the map memory blocks is less than the average erase count of the data memory blocks and a difference between the average erase count of the map memory blocks and the average erase count of the data memory blocks is greater than a first threshold; and perform a garbage collection operation on the detected first victim memory blocks, map data stored in hot data memory blocks to the first victim memory blocks, and map data stored in cold map memory blocks to the hot data memory blocks.