This paper presents an efficient hybrid method consisting of Lorentz reciprocity theorem, finite-difference-time-domain (FDTD) method, thin wire model, transmission line (TL) equations and transfer impedance model, which can be utilized to analyze the system-level transient responses of the microstrip antenna system with antenna, metallic enclosures, braided shielded cable, and lumped element, when illuminated by an external electromagnetic pulse (EMP). In order to avoid over-fine mesh generation and repeated modeling of the antenna in multiple simulations, Lorentz reciprocity theorem is employed to extract an equivalent source model of antenna coupling, thereby improving the computational efficiency. Then, the transfer impedance model and thin wire model are incorporated into the FDTD-TL method efficiently to deal with the back-door coupling through the shielding layer of feeding coaxial cable. Finally, the hybrid FDTD method combined with the extracted equivalent source of antenna coupling is utilized to solve the coupling responses of the whole antenna system. The results of numerical simulation are verified by comparing with the simulation results of CST CS. Then, considering the influence of different incident conditions of external EMP, the characteristics of the coupling response of the system are analyzed. The obtained coupling response information demonstrate that the proposed method is available for further designing electromagnetic protection of the inner circuits of the microstrip antenna system against the impact of external EMP.