The all parallel autotransformer (AT) traction power supply system (TPSS) including several subsections is widely used for high-speed railways. Unfortunately, any fault of catenary and negative feeder will cause all subsections power interruption in the whole system. Moreover, due to the nonlinear relationship between the distance and impedance as well as the symmetry of the system, conventional distance protection schemes fail to identify the fault subsection and the fault types. In this paper, a novel segmental power supply scheme is presented, which can switch the catenary and negative feeder at each AT subsection on and off independently. Based on the theoretical analysis of the electrical characteristics of the traction power network, multiterminals synchronous information is applied and a hybrid fault identification method is proposed, which can accurately identify the fault subsection and fault type. Consequently, only the catenary or negative feeder at the fault subsection will be quickly removed from service without the effect on normal operation of other subsections. Therefore, the reliability of all parallel AT TPSS is improved considerably. This method was verified through simulation and laboratory experiments by the case studies.