The invention discloses a control system and method for a V/v traction power supply system negative sequence current. The system comprises a first power supply arm, a second power supply arm, a firststep-down transformer, a second step-down transformer, and a railway power conditioner, wherein the railway power conditioner comprises two AC loops, two converters and a DC loop. The method comprisessteps of detecting instantaneous values of load currents of two power supply arms; obtaining phases and effective values of the load currents of the two power supply arms by using a single-phase phase locked loop; then obtaining a reference instruction active current effective value and a reference instruction reactive current effective value of the two power supply arms, so as to obtain reference instruction currents of the two converters; and obtaining output voltages of the converters through a passive policy according to the reference instruction currents, so as to track and control the output current of the railway power conditioner. A mathematical model of the RPC is converted into a Hamiltonian model, and a simple PCHD mode-based passive control policy is provided. The system has advantages of good robustness, rapid response speed, and simple design.