The late effect of high-altitude electromagnetic pulse (E₃) will cause dramatic changes in the Earth’s magnetic field and form a ground induced electric field. The induced electric field is equivalent to forming a loop between the excitation source and the ground long-distance conductor and the Earth, generating a geomagnetic induction current (GIC). GIC can cause DC bias of the transformer in the traction power supply system, thereby seriously threatening the safe operation of the traction power supply system. Based on the plane wave theory, the layered Earth conductivity model and the circuit model of the traction power supply system, this paper proposes the GIC algorithm of the traction power supply system under the action of E₃, and takes the railway traction power supply system with return line direct power supply as an example. Calculating the system GIC situation shows that the GIC in the traction power supply system under this power supply mode is far greater than the withstand value of the transformer and other equipment in the system. The study provides support for further research on the effect of the traction power supply system under the action of E₃, the selection of our domestic railway equipment, and disaster prevention.