PurposeFlights are often delayed owing to emergencies. This paper proposes a cooperative slot secondary assignment (CSSA) model based on a collaborative decision-making (CDM) mechanism, and the operation mode of flight waves designs an improved intelligent algorithm to solve the optimal flight plan and minimize the total delay of passenger time.Design/methodology/approachTaking passenger delays, transfer delays and flight cancellation delays into account comprehensively, the total delay time is minimized as the objective function. The model is verified by a linear solver and compared with the first come first service (FCFS) method to prove the effectiveness of the method. An improved adaptive partheno-genetic algorithm (IAPGA) using hierarchical serial number coding was designed, combining elite and roulette strategies to find pareto solutions.FindingsComparing and analyzing the experimental results of various scale examples, the optimization model in this paper is greatly optimized compared to the FCFS method in terms of total delay time, and the IAPGA algorithm is better than the algorithm before in terms of solution performance and solution set quality.Originality/valueBased on the actual situation, this paper considers the operation mode of flight waves. In addition, the flight plan solved by the model can be guaranteed in terms of feasibility and effectiveness, which can provide airlines with reasonable decision-making opinions when reassigning slot resources.