Traditional PI control algorithm has been unable to track control signal without static error, as the controlled variable of the active power filter is high frequency harmonic and reactive current. This paper introduces the composite controller which is used to control the output current of APF, in order to improve the accuracy of steady state and dynamic response speed. As for the delay problem introduced by digital control, the effect of delay on current compensation is analyzed, and the solution of harmonic current prediction control is put forward. Based on the analysis of three-level APF model, a Matlab simulation model based on three level space vector modulation (SVPWM) is built, and the algorithm is verified on a 50 kVA prototype. Simulation analysis and experimental results show that composite control based current tracking control can improve the steady state accuracy of APF current inner-loop compared to traditional PI control.