The invention discloses a control system and method of an electric compressor of a new energy automobile. The control system comprises an inverse variation module, an energy conversion module, a voltage distributing module, compressor drivers, a brake energy recovering device and a main controller. The input end of the inverse variation module is connected with the output end of a battery pack, the input end of the energy conversion module is connected with the output end of the inverse variation module, and the voltage distributing module is connected to the output end of the energy conversion module and comprises at least two capacitors arranged in a series-connection mode, wherein one capacitor is adjustable, and the adjustable capacitor is provided with a capacitance value adjusting mechanism. The compressor drivers are arranged at the two ends of the adjustable capacitor, the input end of the brake energy recovering device is connected with the stator end of a car driving motor, and the main controller is connected with the capacitance value adjusting mechanism, a compressor controller and the control end of the driving motor, and the two ends of the battery pack are further provided with staggered voltage-increasing circuits. According to the control system and method of the electric compressor of the new energy automobile, the technical problem that operation of a compressor is instable is solved.