Abstract: The harmonic current detecting from load side is usually taken as reference current for shunt active power filter, but the compensation accuracy is low because of the large variant rate of harmonic current and the additional harmonic generated by the APF itself. A comprehensive compensation algorithm for three phase four wire active power filter based on instantaneous reactive power theory is proposed to solve the above problems for APF, based on which the specific harmonic detection algorithm is adopted to detect the harmonic current and zero sequence current from grid side, and the reactive current and the negative sequence current is calculated from load side, then the comprehensive compensation of harmonic current and reactive power is realized by the deadbeat control through decoupling of three phase bridge and zero sequence bridge. After compensation, the content of harmonic current is low, the phase difference between current and voltage is small, the current in neutral line is close to zero, and the dynamic response is fast. Furthermore, this method is applicable for system with symmetry or asymmetry load, and the experimental results prove the effectiveness of the proposed control strategy.