Provided is a flash memory system supporting flash defragmentation. The flash memory system includes a host and a flash storage device. In response to a flash defragmentation command by the host, the flash storage device performs flash defragmentation by grouping fragments stored in fragmented blocks of a flash memory on a flash memory management unit basis. The flash memory management unit may be a memory block or page. The flash storage device performs the flash defragmentation regardless of the arrangement order of fragmented files stored in the flash memory.