Abstract: Observation is the main technical method of solar physics research. Stepper motor is often used as the driving source of precision structure adjustment in various observation instruments. Stepper motor control system is an important part of the electronic system of solar observation telescope. This paper introduces a multi-axis stepper motor control system independently developed by Huairou Solar Observation Base. The system uses FPGA as the core controller, uses the interrupt processing mechanism and input/output registers to generate multiple TTL square wave signals, and combines the driver to realize multi-axis stepper motor control. The Hall device is used as the position sensor to realize the closed-loop control of the system. In the design, the Hall signal is filtered to improve the signal recognition accuracy. The MFC class library is used to complete the human-computer interaction interface design, and the serial communication protocol is used to realize the information interaction between the computer and the controller. In addition, external storage circuits have been added to the basic functions to improve the overall reliability of the system.