A new method is proposed to identify grounding faults with catenary disconnection in autotransformer（AT） power supply system for electric railways. This method is based on the variation of real time feeder power factor， and a restraint criterion which can be adaptively adjusted by the system harmonics. The feeder protection equipment can identify high-impedance faults caused by grounding with catenary disconnection， which is different from high transition resistance grounding faults. The identification component is able to maintain normal operation even under conditions when there are heavy load， inrush current and other transients. The method is also able to solve the problem associate with conventional protection which may possibly not respond to faults after AT has been separated. Given that the high-speed railway， heavy load railway and the passenger special line have all been using advanced AT power supply patterns， the identification method proposed has significant value in applications. The feasibility has also been proved in practice.