As a suspension for military aircraft, missile has potential for being struck by lightning in special thunderstorm environments. To improve the lightning protection of airborne missiles, a simulation environment of military aircraft with missiles is built in CST software according to the testing methods in SAE ARP5416 standard. The lightning 1A zones are classified through electrostatic field simulation, and the indirect effects of lightning striking on this model are simulated under injection current method. Simulation results show that the head rear edge of missile (metal parts) and tail wing tip of missile are susceptible to initial attachment from lightning. When the head rear edge of the missile is attached by lightning, extremely harsh electromagnetic environment occurs at the radome, and the equipment in the cabin of carbon fiber reinforced plastic (CFRP) can be damaged owing to the strong electric field and the high voltage induced on cables. However, the electric field strength and induced voltage amplitudes on cables can be dropped in two orders of magnitude separately in the condition of aluminum plating inside the CFRP cabin.