Five-phase stepper motor has been widely used in many fields to control the rotation, speed, position and synchronicity. Through the study of the working principle of the new five-phase stepper motor, the control module of stepper motor is designed by using LM3S615 chip of Luminary company. The Pulse Width Modulation(PWM) module from the internal of stepper motor generates timing signal required by driving components, in order to achieve the subdivision driving for drive assembly. The driving component can produce waves with different duty cycles through the configuration, which can produce different current amplitudes in the motor coil internal to achieve subdivision. The five-phase stepper motor model is SGSP(MS)20-85(X). Experiments show that it can achieve accurate control of the stepper motor on step angle, angular displacement, rotation angle and acceleration.