To address the resonance and stability issues associated with a multi-APFs system, a mathematical model of the conventional hybrid multi-APFs system is established. Based on the model, a mathematical theory and dynamic interaction analysis are developed. A scheme for weakening resonance and improving system stability for the hybrid modular APF system is proposed. The multi-APFs system is composed of different types of modular APF. Each module has different LCL filter parameters, switching frequency, and current carrying capacity. Based on the analysis of the dynamic interaction of the hybrid multi-APFs, it is concluded that increasing the output filter inductance can effectively suppress the resonance and coupling between the APFs of different modules. Compared with the current traditional modular APF, the hybrid multi-APFs system can provide a wider current tracking bandwidth, a fast dynamic response speed, and higher capacity utilization. At the same time, theory and simulation results prove the feasibility of the resonance suppression scheme. This work is supported by the National Natural Science Foundation of China (No. 61863023).