A non-volatile memory (NVM) apparatus and an operation method thereof are provided. A mapping table in a main memory is divided into a plurality of sub-mapping tables according to logical address groups. When an access command of a host is processed by the NVM apparatus, at least one corresponding sub-mapping table is selected from the sub-mapping tables according to a logical address of the access command. If the at least one corresponding sub-mapping table is required to be rebuilt, then the at least one corresponding sub-mapping table is rebuilt, and the logical address of the access command is converter for accessing the NVM apparatus according to the at least one corresponding sub-mapping table which has been rebuilt.