A phase-locked loop (PLL) control system based on field programmable gates array (FPGA) is proposed through analyzing the model of three-phase unipolar-driven BLDCM (brushless direct current motor) to enhance the reliability and accurate steady-state speed for magnetically suspended control moment gyroscope (MSCMG). The numerical operation module, PLL module and current-loop control module are designed based on FPGA using very-high-speed integrated circuit hardware description language (VHDL) to realize the control law of the digital system. The pulse width modulation (PWM) generating module for Buck converter, the commutation signal generating module for the inverter and ADC module are designed for driving the motor and sampling the current signal. The PLL is analyzed and optimized in the paper and all the modules are verified using the software of ModelSim and the experiments. The simulation and experiment results on BLDCM of MSCMG show that the stability of the motor velocity can reach 0.01% and 0.02% respectively by the PLL technology based on FPGA, which is difficult to be obtained by conventional proportion integral different (PID) speed control.