The Port Controlled Hamiltonan(PCH) system model of three-phase three line shunt Active Power Filters(APF) is derived. Based on the model and the characteristic of PCH system, the outer current tracking strategy of three-phase three line Active Power Filters is designed using the passive theory, which is also proved the stability. The problem of tracking complex current with inter harmonics by three-phase three line Active Power Filters can be achieved by this strategy. At last, the simulation platform of system is build, which suggests that inter harmonics current can be tracked by this strategy.