With the increase of air transportation, some crossing waypoints (CWPs) are becoming bottlenecks in the operation of air traffic networks. This paper presents a CWP operation optimisation framework based on a two-stage optimisation method. First, we considered the interests of airlines and air traffic controllers and established a flight-level dynamic allocation model for the CWP to minimise the flight-level deviation and the number of flight conflicts. A multi-objective, self-adaptive differential evolution-local search hybrid algorithm was used to solve the model in a parallel computing manner. Subsequently, a flight conflict resolution algorithm based on the Monte-Carlo tree search was designed for flight conflicts that existed after the optimisation. Finally, based on real operation data, four experimental scenarios were constructed, and the air traffic operation simulation system was used for experimental validation. For daily traffic and 1.2 times peak traffic scenarios, the average flight-level deviation reduction rates after optimisation were 53% and 39%, and the successful flight conflict resolution rates reached 89% and 75%, respectively. The experimental results showed that this optimisation framework can effectively balance the number of flight conflicts with the efficiency of flight-level usage and directly improve the capacity of the CWP, which can be used as a reference for air traffic control auxiliary decision support systems.