In order to solve the problem that the high-pressure sterilization system cannot remove multiple strains at the same time, this article uses a modular design to establish a sterilization system structure that eliminates three strains (Penicillium, yeast, Escherichia coli), and establishes a bipolar square wave and a high-frequency pulse with adjustable frequency Equivalent model of power supply and processing room, respectively. The system can output multiple bipolar square wave waveforms with different peak values when the frequency is 100~1 000 Hz with the pulse width of 10 μs, and can sterilize different pathogens separately. Simulation results show that the power supply can generate three pulses with amplitudes of 4.417, 6.153 and 9.663 kV, respectively, at 100 Hz stable operation, and can generate three pulses with amplitudes of 4.272, 6.082 and 9.393 kV, respectively, at 1 000 Hz stable operation. When the treatment room spacing is 3 mm, the best treatment voltage peaks of Penicillium, yeast, and E. coli are 3.75, 6.00 and 9.00 kV, respectively. Therefore, the three voltage pulses generated during stable operation of the power supply can meet the requirements for simultaneous eradication of Penicillium, yeast and E. coli.