In this paper, based on the “back-door” coupling problem of the electromagnetic pulse, the high-efficiency numerical simulation method based on CP-FDTD is proposed. On the basis of proving the accuracy of CP-FDTD, the detailed analysis of the incident electromagnetic field polarization direction, incident angle and calculation efficiency is carried out, and the applicability of CP-FDTD in the processing of complex slot electromagnetic pulse coupling is verified. By integrating the CP-FDTD algorithm into the self-developed software JEMS-FDTD, a numerical simulation method can be formed to efficiently analyze the shielding effectiveness of engineering complex slots, and it is applied to the shielding effectiveness analysis of engineering component structures.