Abstract: The present invention discloses a flash memory controller and a control method thereof. The flash memory controller comprises a scrambling circuit and a control circuit. The scrambling circuit scrambles at least one input data for generating at least one valid data. The control circuit receives at least one invalid data and the valid data generated by the scrambling circuit. The invalid data is not a fixed constant. The control circuit writes the valid data to at least one valid storage zone of a flash memory and the invalid data to at least one invalid storage zone of the flash memory. By writing non-fixed-constant invalid data to the invalid storage zones of the flash memory, the interference of the invalid storage zones on the valid storage zones may be decreased. Thereby, the reliability and the usable storage space of the flash memory may be increased.