The present invention provides a control method of the flash memory controller. In the control method, by establishing a valid page count table, a detailed valid page count table and/or a zone valid page count table according to deallocate command from the host device, the flash memory controller can efficiently and quickly determine if any one of the zones does not have any valid data, so that the flash memory controller can recommend the host device to send a reset command to reset the zone. In addition, after receiving the reset command from the host device, the flash memory controller can use a garbage collection operation or directly put the blocks corresponding to the erased zone into a spare block pool, for the further use.