To solve power quality problem in V/V traction power supply system, a novel electrical magnetic hybrid power quality compensation system based on railway power conditioner (RPC) and magnetic static var compensator (MSVC) is proposed in this study. The RPC is only used to transfer active power and suppressing harmonics. The MSVC is used to compensate reactive power and suppress 3rd and 5th harmonic currents. The proposed hybrid compensation system will reduce the capacity as well as the DC-link voltage of RPC. The principle of negative, reactive and harmonic currents compensation is analysed first. And then, a collaborative control strategy is proposed to make the compensation system have a fast respond speed. At last the simulation and experiment results have verified the proposed structure and its control strategy effectively.