In order to solve the problem of negative sequence current, harmonic current and electric phase splitting in high-speed railway power supply system, a novel co-phase power supply system based on Double Star Multilevel Power Flow Controller (DS-MPFC) and YNvd balanced transformer is proposed in this paper. This DS-MPFC which consists of four H-Bridge links is AC-AC conversion circuit structure and no direct current bus capacitance is required. Different from the conventional power flow controller based co-phase power supply systems, this system integrates DS-MPFC into the phase-β side flexible taps of YNvd balance transformer instead of into phase-b side via a step-down and isolation transformer, thus the costs are reduced significantly. The topology structure and the working principle are analyzed, furthermore, a synthetical control strategy is proposed. The simulation results show the feasibility and effectiveness of the proposed method. This work is supported by National Natural Science Foundation of China (No. 51477046).