Aiming at the problems of difficult handling of three-dimensional flight conflicts and unfair distribution of resolution costs, we propose a multi-aircraft conflict resolution method based on the network cooperative game. Firstly, we establish a flight conflict network model with aircraft as nodes and the conflict relationship between node pairs as edges. After that, we propose a comprehensive network index that can evaluate the effect of resolution strategy. Based on the concept of “nucleolus solution”, we establish a conflict network alliance with all nodes as participants, and balance the interests of all participants through the resolution cost function. In order to improve the timeliness of the method, we propose two optimization methods: adjusting high-priority nodes and customizing the initial resolution scheme. Finally, we combine the NSGA-II algorithm to solve the optimal conflict resolution scheme. The simulation results show that our method can adjust 10 aircraft in 15.17 s and resolve 12 flight conflicts in a complex conflict scenario containing 40 aircraft; our method reduces the resolution cost by more than 22.1% on average compared with the method without considering the resolution cost. The method ensures both the conflict resolution capability and the reduction in resolution cost.