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For harmonic compensation, a control system of a four-wire three-level NPC inverter employed in a hybrid active power filter (HAPF) based on modulation ratios of switching functions is proposed in this paper. The inverter and two parallel passive filters (PPFs) tuned in 5th and 7th orders of harmonic currents form the HAPF. The PPFs are used for compensating of average reactive power of loads and filtering of 5th and 7th orders of harmonic currents to decrease rated power of the inverter. The switching functions of the inverter control system are extracted based on compensation of variable load reactive power and the orders of harmonic currents with exception of 5th and 7th orders. The averaged model of the inverter is extracted by possible switching states of the inverter's IGBTs. The proposed control method is applicable under asymmetrical non-sinusoidal source and non-linear loads conditions. The principles of the presented control method are analyzed in this paper too. The proposed control method was simulated and the simulation results are provided to validate effectiveness of the proposed control method.