At present, efficient time domain numerical methods used for the coupling effect analysis of electromagnetic pulse to long rails on infinite ground are still rare. An efficient time domain hybrid algorithm, consisting of the finite difference time domain (FDTD) method, the transmission line equation and the fast calculation method for the excitation fields of the long rails, is presented to realize fast electromagnetic pulse coupling simulation of the long rails with compensation capacitance in time domain. Firstly, to avoid direct modeling of the irregular structures of the rails, the rails are equivalent to the tubular conductor models based on the skin effect, and the corresponding per unit length distribution parameters are extracted. Then, the electric field distribution along the rails are calculated via the fast calculation method for the excitation fields of long rails rapidly, and the electromagnetic coupling model of the rails with compensation capacitance is constructed by the transmission line equation. Finally, the FDTD method is used to solve the transmission line equation to obtain the electromagnetic pulse coupling responses on the rails. The results show that the width of the coupling current waveform on the rails would extend, and the peak values of these currents would saturate with the rail length increasing to a certain value. This conclusion will provide important data for the electromagnetic protection design of track circuit system.