The present invention provides a control method of a flash memory controller, wherein the flash memory controller is configured to access a flash memory module, the flash memory module includes a plurality of planes, and each plane includes a plurality of blocks; and the control method includes the steps of: after the flash memory controller is powered on, reading a first code bank from a specific block of the plurality of blocks; storing the first code bank into a buffer memory; executing the first code bank to manage the flash memory module; when the flash memory controller starts a code bank swapping operation, trying to read a second code bank from a super block; if the second code bank is read successfully, storing the second code bank into the buffer memory to replace the first code bank; and executing the second code bank to manage the flash memory module.