In order to realize the high reliability and low-cost application of the space two-dimensional turntable in orbit, as well as the ability of low-speed smooth motion, high-precision tracking and 360 degree full range continuous operation, a vector control system of stepper motor based on FPGA chip is established. The 128 subdivision precision control of stepping motor is realized by PWM chopping adjustment of current sine table. A 21 bit photoelectric encoder used as position feedback and a harmonic reducer used as mechanism drive to realize open-loop control, real-time speed adjustment and tracking control, optimal path planning control and motion timeout protection . The influence of MOSFET on chopping frequency and maximum subdivision is analyzed. The experimental results show that the tracking accuracy of the two axes is better than 0.005 degrees at 3σ, the speed stability is less than 5%, and the servo control bandwidth is more than 4Hz, and it has the ability of continuous zero crossing. The control system can simplify the hardware design, increase the applicability of software, more suitable for ultra-low speed motion, and meet the requirements of two-dimensional turntable for servo control system.