In order to allocate airport flight time resources more scientifically and reasonably, a flight time optimization method considering transit passengers is proposed. First, a flight connection quality assessment model considering the effectiveness of candidate trips is constructed by combining the travel choice characteristics of transit passengers. Second, a dual-objective model is established to maximize the flight connection quality and minimize the maximum flight time offset, and constraints such as the type of transit passengers and the type of connecting flights are taken into account, so that the optimization model is more in line with the actual transit operation situation of hub airports. Finally, an adaptive large neighborhood search algorithm is designed to solve the problem, and the model and algorithm are applied to Beijing Capital International Airport for case study. The results show that the constructed model can provide passengers with more effective trips, increase the number of reachable airports, and improve airport connectivity based on the differences in the choices of transit passengers in terms of time, space, the impact of direct flights, and service quality. The optimized effective passenger journeys and flight connection quality have been improved by 21.74% and 21.57% respectively, and the connection quality of about 79.66% of the flights has been improved. It can be seen that the optimized flight schedules are more reasonable in terms of temporal and spatial distribution, which can significantly improve the quality of connection between flights and provide more effective transfer options for transit passengers.