A controlling method of a rewritable non-volatile memory module, and a memory controller and a data transmission system using the same are provided. The controlling method includes following steps. A command is received from a host system. Whether the command is a configuration command is determined according to a command code of the command. A plurality of action information in the configuration command and an execution sequence corresponding to the action information are analyzed. The action information is executed according to the execution sequence. Each action information is configured to request the rewritable non-volatile memory module to execute a predetermined action. Thereby, the functionality of a memory storage device can be dynamically extended.