The present invention provides a flash memory controller, wherein the flash memory controller is arranged to access a flash memory module, the flash memory module includes a plurality of flash memory chips, the flash memory controller includes a buffer memory and a microcontroller, and the buffer memory is arranged to store an in-system programming (ISP) code. When the flash memory controller enters a power saving mode, the microcontroller disables a portion of the buffer memory to make at least one portion of the ISP code disappear; and when the flash memory controller enters a normal mode from the power saving mode, the microcontroller reads said at least one portion of the ISP code from N flash memory chips within the plurality of flash memory chips, wherein N is a positive integer greater than one.