A system operation method for controlling a rewritable non-volatile memory module is provided. The rewritable non-volatile memory module includes a plurality of physical blocks. The system operation method includes following steps. A first signal is received from a host system through a host interface. Whether a system setting of the host interface is to be modified is determined. If the system setting is to be modified, a system parameter is read from the physical blocks, and the system setting is modified according to the system parameter. A second signal is transmitted to the host system to establish a connection recognition between the rewritable non-volatile memory module and the host system. Thereby, the settings of transmission between the host system and the rewritable non-volatile memory module are made more flexible.