Provided herein are a memory system and an operating method thereof. A method of operating a controller for controlling a memory block including a plurality of pages includes determining whether the memory block is in an open state or a closed state, if the memory block is in the open state, reading merged metadata included in the plurality of pages, and rebuilding logical to physical (L2P) mapping data of a plurality of logical pages included in each of the plurality of pages based on the merged metadata.