A method for operating a memory system includes detecting a size of a data requested by a host, generating a first data that represents the size of the requested data and a second data that represents a remaining empty space other than a space for the requested data in a first region having a unit size of data storage in a memory device when the size of the requested data is smaller than the first region and the request is to write the requested data into the memory device, and storing the first data and the second data in the memory device along with the requested data.