A flash memory storage system is provided. The flash memory storage system includes a controller having a rewritable non-volatile memory and a flash memory chip. The rewritable non-volatile memory stores a data token and the flash memory chip stores a security data and a message digest. When the security data in the flash memory chip is updated, the controller updates the data token and generates an eigenvalue, and updates the message digest according to the updated data token and the updated eigenvalue by using a one-way hash function, respectively. When the security data in the flash memory chip is processed by the controller, the controller determinates whether the security data is falsified according to the data token, the eigenvalue and the message digest. In such a way, the security data stored in the flash memory storage system can be effectively protected.