The invention provides an energy storage unit and APF combined system. The energy storage unit and APF combined system is characterized by comprising a sampling and conditioning system, a DSP control system, a driving system, a main circuit system and a protection system. A working method of the energy storage unit and APF combined system includes the steps of real-time detection, signal conditioning, compensating signal transmitting, signal conversion, computing and processing, state detection and correct operation. The energy storage unit and APF combined system and the working method have the advantages that the structure is simple, and the method is easy to understand; multiple purposes are achieved through one machine, harmonic waves can be treated, and power balance can be adjusted; the stability of busbar voltage is improved; the reliability of the combined system is improved; application prospects are good, and engineering application value is high.