Based on a two-phase hybrid stepping motor control system, this paper applies sliding mode control algorithms to position control to improve system dynamic performance and anti-interference performance. Meanwhile, in order to reduce the chattering problem in sliding mode control, a time-varying boundary layer control algorithm is designed, and based on constant velocity approach law, the time-varying boundary layer algorithm is applied to motor position control system. Simulation experiment verification is carried out through MATLAB/Simulink, and the actual experiment is further completed. It is proved that the control algorithm proposed in this paper can significantly reduce the chattering problems in traditional sliding mode control, and has good dynamic performance. Through comparison experiments, the control algorithm applied in this paper is compared with the traditional PID control under sudden load, which shows the superiority of the two-phase hybrid stepping motor position control system with time-varying boundary layer sliding mode control algorithm.