Due to the parameters of the controller were fixed, the control effect of permanent magnet synchronous motor position servo system was not satisfying. So we design a fuzzy logic controller based on bacterial foraging optimization algorithm (BFOA). Based on the theory of space vector control, the position control system was three closed loop control system of permanent magnet synchronous motor which was consisted of the position loop, speed loop and current loop. The fuzzy logic controller was applied to the position loop in the MATLAB/Simulink environment. The simulation results showed that compared with the traditional PID method, the fuzzy control scheme based on BFOA had better control quality and stronger ability of restraint interference, and could effectively improve the rapidity and accuracy of the motor position control.