The embodiments of the present disclosure relate to a memory system for managing data corresponding to a plurality of zones and operating method thereof. According to embodiments of the present disclosure, the memory system may include i) a memory device including a plurality of memory blocks each including a plurality of pages, and ii) a memory controller configured to write data corresponding to a plurality of zones to a first area including two or more of the plurality of memory blocks, flush the data corresponding to a first zone among the plurality of zones to a second area including two or more of the plurality of memory blocks on determination that a flush condition set for the first zone is satisfied.