In response to the complex electromagnetic interference problem of connecting equipment and external radiation sources in the wiring harness of aircraft airborne platforms under lightning strike environment, considering the impact of different structures of the wiring duct on the protective performance of the wiring duct, based on the three axis method and combined with the Van Helvoort shape coefficient, a theoretical expression for the transfer impedance of the wiring duct from low frequency to high frequency state is derived. Furthermore, a simulation model for the protection of wire ducts with different aspect ratios is established to study the protection performance of wire ducts with different shapes and sizes. Finally, a lightning electromagnetic protection simulation model was established for the internal trunking of the composite material fuselage, analyzing the protective effects of different positions and shapes of trunking on the fuselage, and further verifying the differences in the protective performance of different structural trunking. The results show that for every 1/2 increase in aspect ratio, the shielding effectiveness of the trunking increases by about 5 dB, and the effective protection area gradually expands. As the distance between the body and the skin increases, the induced current of the cables inside the body decreases linearly. The sealing performance of the trunking is directly proportional to its protective performance.