Abstract: Carbon fiber reinforced polymer (CFRP) composites are highly susceptible to lightning strike damage, posing a serious threat to flight safety, while existing protection schemes remain inadequate in terms of current dissipation efficiency and multifunctional integration. In this study, two carbon nanotube film (CNTF) configurations were designed: a surface configuration (SCNTF/CFRP) and an interlaminar configuration (ICNTF/CFRP). Through simulated lightning strike tests and electrical-thermal-mechanical multiphysics coupled simulations, the protection mechanisms and performance differences between the two configurations were systematically investigated. Results show that SCNTF/CFRP achieves rapid lateral current dispersion via the surface conductive network, demonstrating superior lightning strike protection: compared with unprotected CFRP, the damage depth was reduced by 39%, the damage area decreased from 33 cm² to 1.6 cm² (a 95% reduction), the post-strike flexural strength retention reached 86.12%, and the electromagnetic shielding effectiveness (EME) in the X-band reached 84 dB. Damage analysis further revealed that lightning strike damage follows a dual mechanism of "central thermal degradation and peripheral thermal stress". In contrast, ICNTF/CFRP exhibited limited lightning protection performance due to stress concentration at the interlaminar interface (damage area reduced by only 3%), whereas its interlaminar structure conferred superior electromagnetic shielding effectiveness of 97 dB in the X-band. These findings indicate that the SCNTF configuration is better suited for lightning strike protection applications, while the ICNTF configuration is more appropriate for scenarios with higher electromagnetic shielding requirements, providing theoretical guidance for the multifunctional lightning protection design of aeronautical CFRP structures.