Aiming at the low confidence in the dynamic configuration ofterminal check-in system to minimize the sum of facility usage costs and passengers time costs, a multi -objective optimization method is proposed. The multi-objective algorithm was applied to the dynamic configuration process of check-in system. The optimization targets of counter operating costs and check-in waiting time for airlines and passengers were set respectively, and dynamic configuration model of terminal check-in system was built to configure the opening number of Disland check-in counters in the Nanjing Lukou International Airport Terminal 2 dynamically.The NSGA-Ⅱ algorithm was employed to obtain the Pareto optimal solution, at the same time, a posteriori evaluation based on TOPSIS was used to compare and analyze the different configuration schemes. Finally, the dynamic configuration results of the D-island check-in system for the whole day were obtained. The research effectively eliminates the difference between cost and time dimensions, which is beneficial for airlines and airports to achieve unique optimization strategies and provides a new method for dynamic configuration of check-in resources.