Military aircraft R&D projects require large-scale investment in cost and time, and involve a complex coordination process in decision-making. The R&D project manager should determine the development management priorities as accurately as possible and focus on R&D capabilities, thereby reducing the risks of the aircraft R&D project. To this end, this study aims to reduce R&D risk by prioritizing cost, schedule, and performance, which are basic management factors used in R&D project management in defense project management regulations. Analytic Hierarchy Process (AHP) is applied using a questionnaire for managers in charge of aviation R&D under the Defense Acquisition Program Administration. As a primary result, the importance of the factors that the aircraft R&D project manager should consider was derived in the order of performance, cost, and schedule, and the priorities of performance and cost in the lower layer were also identified. In addition, in order to provide practical risk management measures to aircraft R&D project managers, the results of analyzing 28 cases of US National Transportation Safety Board accidents were compared and analyzed with the AHP analysis results, and management measures suitable for the situation were specified.