The existing problems of the traction power-supply system (i.e., the existence of the neutral section and the power quality problems) limit the development of railways, especially high-speed railways, which are developing rapidly worldwide. The existence of the neutral section leads to the speed loss and traction loss as well as mechanical failures, all of which threaten the fast and safe operation of the train and the system. Meanwhile, the power quality problems (e.g., the negative sequence current, the reactive power, and the harmonic) can bring a series of problems that cannot be ignored on the three-phase grid side. In response, many researchers have proposed co-phase power-supply schemes to solve these two problems simultaneously. Given that the auto-transformer (AT) power-supply mode has become the main power-supply mode for the high-speed railway traction power-supply system, it has a bright future following the rapid development of the high-speed railway. In addition, there is no co-phase power-supply scheme designed for AT power-supply mode in the existing schemes. Therefore, the main contribution of this paper is to propose a specifically designed power-supply mode more suitable for the AT, as well as to establish the control systems for the rectifier side and the inverter side. In addition, for the proposed scheme, the operation principle is analyzed, the mathematical model is built, and the control system is created, and its functionality is verified by simulation, and its advantages are compared and summarized finally. The result proves that it can meet functional requirements. At the same time, compared with the existing co-phase power-supply scheme, it saves an auto-transformer in terms of topology, reduces the current stress by 10.9% in terms of the current stress of the switching device, and reduces the power loss by 0.25% in terms of the entire system power loss, which will result in a larger amount of electricity being saved. All of this makes it a more suitable co-phase power-supply scheme for the AT power-supply mode.