It is proposed in this paper the control system of a MEMS stronglink for PC authentication system, which is composed of MEMS stronglink, interface card and dedicated software. The stronglink is comprised of a multitry countermeshing gears (CMG) discrimination device based on micro electromechanical system (MEMS) technology. The control system is consist of micromotor driving system, electrical control system and dedicated software program. The PCI7248 DIO extending card and L6234 brushless DC motor driven IC are applied for the control of MEMS stronglink. The authentication system on PC startup is controlled by the program in BIOS chip, which gets the control during the POST of PC. The discrimination device has the function of automatic resetting with correct code, which can be tried 3 times. The success rate in 1000 times is 100%.