The leaked stray current during the metro operation causes a change of the nearby surface potential, which results in a variation of the ground potential of grounding transformers, then the transformer DC bias. By studying the stray current leakage mode in the traction power supply system for rail transit and the flow path which causes the transformer DC bias, the mechanism of transformer DC bias generated by the metro stray current is revealed. With the consideration of the action mechanism of stray current on transformer DC bias, the equivalent resistance model of the transformer DC bias caused by the stray current is built with doubleend power supply which is based on the discrete model of the stray current distribution. The mathematical equation of the transformer neutral point current with the changing operating conditions of the rail transit is established, and the numerical calculation of the transformer neutral point is realized. The validity of the model is verified by the CDEGS simulation, which has certain guiding significance for the planning and construction of subway stations and substations.