This paper studies the flight path optimization problem of air cargo companies in aviation line alliance. Considering the influence of alliance on operation, the selection probability of air alliance is introduced. It proposes a directed aircraft fleet routing problem optimization multiple-objective model (SMADDAAAFRPTW) with multi-airbase stochastic and time constraints to minimize total operating cost and service level maximization. Using improving NSGA-II algorithm, introducing hybrid quantum evolution algorithm and genetic engineering into cross-mutation. Comparing with the weighted method, it shows that the improved NSGA-II algorithm is effective and has better computational efficiency. The results show that the optimal number of bases and the optimal number of aircraft according to the change of service level of unit cost reduction. As a whole, with the increase of load capacity and fixed cost on aircraft, cost is getting higher and higher, service level is getting lower and lower. The larger the cost of self operation, the larger the total cost and the higher the service level; the smaller the outsourcing cost, the smaller the total cost, and the lower the service level. With the increase of penalty cost, the total cost and service level have little change.

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