The passivity based hybrid controller which can adjust the damping injection online through fuzzy control theory is designed based on the Port Controlled Hamiltonian with Dissipation (PCHD) mathematical model of Active Power Filter (APF) and through the method of Interconnection and Damping Assignment Passivity Based Control (IDA-PBC) to improve the current compensation effect of APF. While self-adaptive fuzzy PI control method is used in order to adjust the proportional and integral coefficient online to improve the DC side voltage control performance of APF. Using the controller proposed, the source current can be compensated and the load harmonic current can be suppressed effectively, which makes the power supply current sinusoidal and gets a better dynamic and static performance of DC voltage. The simulation models of APF and the self-adaptive fuzzy-passivity based hybrid control system are built based on Matlab/Simulink. The harmonic compensation performance of APF is simulated and analyzed. The simulation results show that the self-adaptive fuzzy-passivity based hybrid control strategy proposed is feasible. This work is supported by National Natural Science Foundation of China (No. 51777012 and 51477011).