By analyzing the basic working principle of six-phase permanent brushless direct current motor, this paper seeks to derive from it the voltage equation, back electromotive force equation, torque and motion equation, followed by the establishment of corresponding mathematical models. Based on the established mathematical model, the simulation model of control system is built in Matlab/Simulink. The simulation results verify the correctness and feasibility of the system control, thus providing the basis for the research and design of practical multi-phase brushless DC motor control system.