Abstract: The paper put forward a design scheme of control system with double closed loops of three-level SAPF. The system uses ip-iq method to extract harmonics and uses instantaneous reactive power theory to detect three-phase voltage and load current, so as to calculate compensation current. The voltage loop is controlled by fuzzy PI controller and current loop is controlled by internal model controller. Meanwhile, the system adopts three-level SVPWM modulator to output compensation current. The simulation experiment result showed that the system has good harmonic compensation effect.