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In order to solve the problem of poor control effect and low control precision of the master-slave arm caused by signal interference in the motion process of minimally invasive surgery robot, a motion control system design of minimally invasive surgery robot based on STFT is proposed. The main controller is connected with the host computer through Bluetooth wireless transmission mode. The I/O port is used to simulate SCI hardware flow control mode to realize the communication between MCU and Bluetooth and provide basic data for the system. The parallel oscillation mode of clock reference circuit is designed to facilitate the restart of out of control program. According to the structure of motion controller, A/D conversion interface is designed and analyzed in detail. The STFT based short-time Fourier transform method is used to suppress external interference, and the control process is designed with the support of LM629 Motion Control ASIC. The motion control system of minimally invasive surgery robot based on STFT is designed. The experimental results show that the system can accurately control the motion accuracy of minimally invasive surgery robot, and provide equipment support for the intelligent development of medical surgery.