Aiming at the common working conditions that have accurate requirements for the running time and distance of the stepping motor in production, a set of S-curve control algorithm for the stepping motor is designed, which can flexibly set the motion process according to different operation requirements, and use fewer parameters to plan the whole motion path, so as to achieve the ideal motion effect. A new cosine S-curve is designed, and the MATLAB/Simulink simulation control model and hardware test system are built for simulation and practical verification. The results show that the actual acceleration and deceleration process of the motor runs smoothly and starts stably, and the vibration is small. It can run accurately under the set parameters. Compared with the direct start and stop, the operation effect is greatly improved. It has been applied in an automatic numbering machine project.