A non-volatile memory device is configured to perform automatic boundary alignment between logical access units of a file system and physical access units of the non-volatile memory device. The file system of the non-volatile memory device is configured to include a partition having a system data area and a user data area which comprises a plurality of logical access units. The boundaries of the logical access units in the partition are aligned with the boundaries of physical access units of the non-volatile memory device. Unnecessary data access may be reduced without introducing an additional mapping table or re-formatting storage space in the partition.