The interconnectivity of avionics systems supports the need to incorporate functional safety and information security into airworthiness validation and maintenance protocols, which is critical. This necessity arises from the demanding operational environments and the limitations on defense resource allocation. This study proposes an optimization model for the strategic deployment of defense mechanisms, leveraging the dynamic interplay between attack and defense modeled by non-cooperative game theory and aligning with the maintenance schedules of civil aircraft. By developing an Attack–Defense Tree and conducting a non-cooperative game analysis, this paper outlines strategies from both the attacker’s and defender’s perspectives, assessing the impact of focused defense improvements on the system’s security integrity. The results reveal that the broad expansion of defense measures reduces their effectiveness, whereas targeted deployment significantly enhances protection. Monte Carlo simulations are employed to approximate equilibrium solutions across the strategy space, reducing computational complexity while retaining robustness in capturing equilibrium trends. This approach supports efficient allocation of defense resources, strengthens overall system security, and provides a practical foundation for integrating security analysis into avionics maintenance and certification processes.