Aiming at the fact that the traction network boundary of the through-type co-phase auto-transformer (AT) traction power supply system has a strong attenuation effect on high-frequency transients, a single-ended current direction transient protection method of traction network based on morphology is proposed. The multi-resolution morphological gradient is used to process the fault transient current detected at the protection installation, and the polarity of the mutation point of the line mode component is obtained, which constitutes the directional start element. If the polarity is negative, the fault occurs outside the local area, and the protection does not operate. If the polarity is positive, it is necessary to further calculate the morphological spectrum of the fault current line mode component, and convert the normalized morphological spectrum to the frequency domain. By comparing the size of the morphological spectrum value and the threshold in the frequency domain, the fault is judged to be an internal fault or an external fault on the opposite side. The through-type co-phase AT traction power supply system is built on PSCAD, and plenty of fault simulations are conducted for different situations. The simulation results show the availability of the protection method.