Various missions significantly impact the fleet’s level repair plan. The mission requirement model is established based on the “regular and dual control” repair mode. Considering the fleet’s overall operation, capability decay characteristics, and planner’s expectations and preferences, the fleet’s capability evaluation model is constructed. Furthermore, aiming at the maximum capability value and the minimum number of the mission ships and comprehensively considering constraints such as sailing rate, mission period, repair period, repair cost, capability restoration, and mission capability, the optimization model of the fleet’s level repair plan for diverse missions is established. The particle swarm optimization algorithm based on the hierarchical sequence method is used to solve the model, and the fleet’s level repair plan and mission configuration plan are obtained, which solves the coordination problem of the two types of plans. The results show that, compared with the traditional planning method, this method can fully consider the actual requirements of diverse missions and has better coordination of the relationship between the ship’s use and repair. This method can provide strong technical support for the scientific preparation of level repair plans and the effective completion of combat readiness training missions.