In order to improve the control performance of the module of the inverting circuit, a control method of the inverting circuit based on integral separation and deadtime PID control was proposed. This control method could effectively solve the problem that the control quantity caused by the traditional PID control exceeded the controlled object, thus leading to the system oscillation. Integral separation and deadtime PID control algorithm introduced deadtime PID control algorithm into integral separation PID control algorithm. By combining the advantages of the two control algorithms, it could not only prolong the service life of the control system, but also limit the system deviation. Finally, the simulation model of high frequency power supply with inverting circuit module was established by MATLAB/Simulink, and the effectiveness and practicability of the proposed PID control method were verified.