The purpose of this paper is to analyze the working principle of folding machine and it also explains the working mode of the stepper motor. Basing on these, the control-system of folding machine is designed. It is through the AT89C52 MPU and the corresponding circuit of periphery to control the two stepper motors. So it can drive the feeding roller and the paper roller to overlay in accordance with the predefined size. The system achieves the automation of folding. It not only reduces the labor, but also improves the efficiency and accuracy of folding. It has a very broad application prospect.