Based on a two-phase hybrid stepping motor control system, the article applies sliding mode control algorithms to position control to improve system dynamic performance and anti-interference performance. At the same time, in order to reduce the chattering problem in sliding mode control, Firstly, a time-varying boundary layer control algorithm is designed, and based on constant velocity approach law, applying time-varying boundary layer algorithm to motor position control system. Then carried out simulation experiment verification through Matlab / Simulink, and further completed the actual experiment, It is proved that the control algorithm proposed in the paper can significantly reduce the chattering problem in traditional sliding mode control, and has good dynamic performance. Finally, through comparison experiments, the control algorithm applied in this paper is compared with the traditional PID control under sudden load,which shows that the two-phase hybrid stepping motor position control system with time-varying boundary layer sliding mode control algorithm does have certain advantages..