A memory system includes a memory device including a plurality of memory blocks each block including a plurality of pages; and a controller including a memory, and suitable for buffering segments of user data and metadata for a command operation into the memory, and storing the buffered segments into a super memory block including two or more of the plurality of memory blocks during the command operation in response to a command, wherein, when the total size of to-be-stored data among the buffered segments of the memory is smaller than an unit size of the one shot program, the controller stores dummy data as well as the to-be-stored data into the super memory block.