Passivity-based control（PBC） strategies provide a solution to reinforce transient stabilization of active power filters（APF） with variable nonlinear loads. In this paper， a novel PBC method is developed to force the three-phase shunt APF to track the reference harmonic current of time-varying nonlinear loads. As non-offseted“workless forces” determined， a fully defined control rule is presented to obtain the full stability and current tracking control. For the purpose， Euler-Lagrange model of shunt APF system is determined firstly. A novel current tracking dynamic controller with PBC scheme is then implemented. Combined with nonlinear parameter estimator， the developed PBC system not only has the advantages of simple control structure， but also reduces the harmonic current tracking error caused by resistance variation， which enhances the robustness of the APF control system. The reasonability and validity are testified by the experimental results based on dSPACE.