In order to realize the scanning requirements of the two-dimensional multi-axis differential absorption spectroscopy (MAX-DOAS) instrument, a control system for prism scanning is designed based on STM32 microprocessor and photoelectric encoder with the two-phase stepper motor driver chip TMC261 as the core. The requirements for rotational accuracy and resolution of two-dimensional MAX-DOAS external prism are analyzed, and then the system scheme is expounded from the two aspects of control system structure design and concrete implementation process. Measurement experiments are carried out to evaluate the actual effect of the designed system. Results show that the subdivision of the rotational stepping angle of the prism can be adjusted within the range from 0 to 256, the scanning resolution is up to 1.8°/256, the position accuracy error is less than 5%, and the absolute value of step angle accuracy error is less than 8%. It indicates that the designed scanning control system has a broad application prospect in optical instruments.