Throughout the world, the reliability-based approach to safety design of aircraft systems is quite mature and widely used. However, there are still shortcomings in the reliability-based aircraft system safety analysis method. It cannot dynamically analyze the accident evolution process and lack consideration of the complex situation of multifactor coupling. On the basis of the original aircraft system safety analysis method, this paper innovatively proposes a functional hazard analysis (FHA) method based on the analytic hierarchy process (AHP) and multifactor fuzzy comprehensive assessment (FCA). The purpose is to improve the objectivity and quantification of the FHA method in the safety design of aircraft systems. At the same time, in the terminal airworthiness verification, this paper proposes a repeatable and controllable virtual test flight verification method, which aims to reduce the cost and cycle of the terminal airworthiness verification and expand the coverage of the envelope verification. Finally, combined with the clauses in MIL-HDBK-516B, a case calculation is carried out to verify the feasibility of the proposed method.