1. A flash memory storage system, comprising: a flash memory chip, for storing at least one security data, and at least one message digest; and a controller, coupled to the flash memory chip and comprising at least one non-volatile memory, the at least one non-volatile memory is configured for storing at least one data token, wherein the controller generates at least one eigenvalue corresponding to the at least one security data, and the at least one message digest is generated by using a one-way hash function according to the at least one data token and the at least one eigenvalue, wherein when the at least one security data is updated, the controller changes the at least one data token and the at least one eigenvalue, and uses the one-way hash function to change the at least one message digest according to the changed at least one data token and the changed at least one eigenvalue; and when the controller processes the at least one security data stored in the flash memory chip, the controller reads the at least one data token, the at least one eigenvalue, and the at least one message digest, and generates at least one comparison message digest according to the read at least one data token and the read at least one eigenvalue, and determines whether the read at least one message digest is identical with the generated at least one comparison message digest, wherein when it is determined that the read at least one message digest is different from the generated at least one comparison message digest, the controller outputs a warning message.