A negative voltage backflow direct current supply system for a rail transport is provided. The system adds a negative voltage return line and a DC converter for realizing negative voltage backflow current based on traditional DC power supply system. The negative voltage backflow line replaces the backflow line of running rail in the traditional DC power supply system, which can greatly reduce or eliminate the stray current in the traditional DC power supply system and the negative influence of too high ground potential of running rail. At the same time, the DC converter can be used as regenerative braking energy storage device of train to improve the regenerative braking energy utilization efficiency of DC power supply system and maintain the voltage stability of DC power supply system of rail transport.