The scientific and reasonable selection of mission aircraft is an important support to ensure the success of the mission. In view of the characteristics of fuzzy evaluation and combinatorial optimization for multi-stage mission aircraft selection, based on the evaluation index system of mission aircraft combat fitness, the combat fitness of different mission subjects was evaluated based on intuitionistic fuzzy and group analytic hierarchy process (AHP). Then, based on the simulated annealing genetic algorithm, the aircraft selection for multi-phase mission system was realized with the target of combat adaptability of multi-phase mission system. The validity of the model method is verified by case analysis, which provides decision support for multi-phase mission aircraft selection in the first-line troops.