Comprehensive harmonic mitigation techniques have emerged recently, due to the massive and distributed access of nonlinear loads. To achieve the online harmonic mitigation from a system perspective, this paper proposes a system-level control strategy of multiple SAPFs. Firstly, the system control scheme is presented. Then, the analysis of comprehensive harmonic mitigation model is proposed to obtain the optimal SAPFs reference current. Besides, a three-stage online control strategy of SAPFs is designed to achieve the reliable system impedance identification. Finally, the IEEE 18-bus system is applied in simulation and a reduced-scale system is built in experiment. Both results could verify the feasibility and effectiveness of the proposed strategy.