To achieve beam scanning of mechanical phased array antenna, the miniature brushless DC motor is adopted to drive a helical antenna element to rotate to a predetermined radiation phase. A new micro brushless DC motor position control system is designed. A proportional sliding mode surface super twisting algorithm controller is constructed for velocity control, the position PID controller combined with velocity profile strategy is used to realize the intermediate process control of the rotation. Establishing the control system simulation model in Simulink, the feasibility of this scheme is verified, and the control system is constructed on an FPGA hardware experiment platform. According to the results of simulation and experiment, it’s indicated the micro brushless DC motor can drive the antenna to follow the preset velocity profile curve accurately, and the rotation angle reaches 180° within a 50 ms control period. Both the position tracking deviation in the intermediate process and the residual error at the balance position are less than ±3°.