The flight effectiveness evaluation for the autonomous UAV is a critical means to support flight control decisions for flight safety and completing complex missions. However, the whole flight is composed of multiple phases, which shows capabilities on different subsystems and different flight properties. The flight effectiveness will exist discrepancy if the overall analysis is conducted. It is necessary to analyze the flight effectiveness adapted to each phase mission with an accurate evaluation result. Thus, this paper proposes a method of adaptive autonomous UAV flight effectiveness evaluation based on phased missions. Firstly, each flight phase needs to be identified supporting the subsequent evaluation. Then, the evaluation indicator system for each flight phase mission is established according to subsystem health and flight properties. Finally, the adaptive flight effectiveness evaluation model based on the non-binary hierarchy method is modeled to obtain weights of each indicator, which calculates accurate flight effectiveness. Taking the flight of a fixed-wing UAV as an example, the method proposed in this paper is used to complete flight effectiveness evaluation for the ‘climbing’, ‘cruising’ and ‘descending’ phases. Specific decision support can be provided for improving safety and the completion ability of missions for the UAV.