In order to solve the problems of the high cost of air transportation and waste of idle transportation resources, this paper puts forward the research on route optimization of aircraft based on transshipment under route alliance. Firstly, based on the problem of cargo transfer, considering the impact of the alliance on the operation, the selection probability of aviation alliance is introduced to determine the self operation and outsourcing of segment transportation before and after the transfer, and the connection of outsourcing transportation is also considered. The aircraft route optimization model based on transshipment, known as the T-AAAFRP model, is then built in the alliance environment while taking into account the capacity limitation of double airports in the aviation network, the capacity limitation of all cargo aircraft in flight time and airspace in operation, and taking the total cost minimization as the goal Secondly, an adaptive genetic algorithm is used to solve the model. Finally, through a case study, the location and path optimization problems are studied. The results show that the algorithm designed in this paper has high convergence. In the process of changing the number of transfer points, double airport cities are always selected as transfer points. The change of demand and aircraft fixed cost has great influence on optimization decision. The decision to optimize is greatly influenced by changes in demand and aircraft fixed costs. The weight of aircraft, the sharing coefficient of alliance self operation and outsourcing, and the change of decision-maker’s risk preference have little influence on the optimization decision. But on the whole, the larger the number of transfer points, the smaller the total cost and the smaller the number of aircraft used. However, generally speaking, the more transfer sites there are, the lower the overall cost and the fewer aircraft are needed.