The most basic part of FAIMS system is the high field asymmetric RF power supply, which provides voltage difference for the effective separation of ions in the migration region. In this paper, the principle of half bridge inverter is used to generate RF square wave. A three leg square wave generator is designed to reduce the current flowing through the high voltage DC power supply. So the power of the system is reduced effectively. Considering the complexity of FAIMS chip and the portability of the instrument, the differential RF mode is improved, which effectively reduces the input requirements of FAIMS for the high voltage DC power supply and is beneficial to the high voltage DC power supply. It is beneficial to simplify the high-voltage DC power supply and reduce the power consumption, which is conducive to the miniaturization of FAIMS. Combined with automatic scanning of compensation voltage, the optimized high field asymmetric rectangular waveform RF power supply is developed. Through experimental comparison, it meets the requirements of FAIMS migration area.