The coupling of railway power conditioner (RPC), network, and train will change the impedance characteristics of the existing traction power supply systems, which will lead to the unclear law of high-frequency harmonic resonance. This paper aims to study the resonance mechanism of the RPC-network train coupling system, and then solve the resonance problem of the existing traction power supply system from the perspective of reshaping the high-frequency impedance of the system. Firstly, the RPC-network-train coupling system’s dynamic node admittance matrix is established. After that, a comprehensive resonance evaluation method is proposed to obtain the resonance impact factors (RIFs) of multiple virtual impedances in the control strategy and the filtering parameters, which can realize the comparison and selection of five existing impedance reshaping strategies. To ensure the safe and stable operation of the RPC-network-train coupling system, a multi-objective sorting optimization strategy (MOSOS) considering resonance suppression, harmonics filtering, filter cost, and control system stability is proposed for the RPC based on the RIFs. Finally, the effectiveness of the proposed method is verified by the simulation result in MATLAB/Simulink and the experiment result in the StarSim hardware-in-the-loop (HIL) platform respectively.