A mission assignment model of multi-anti-missile combat based on the effectiveness optimization is proposed. First, the relation between mission assignment and target allocation is clarified, based on which the mission generation principle is put forward and the mission assignment model considering the uniformity and coherence performance is established. Then, in order to describe the cooperation of schemes, the basic effectiveness, the self-cooperative efficiency and the inter-cooperative efficiency are defined. At last, the particle swarm optimization (PSO) is used to solve this optimization problem and the simulation shows that the method and the model proposed in this paper are effective in mission assignment problem for cooperative anti-missile combat, and also shows the advantage of mission cooperation in the cooperative anti-missile mission of multi-anti-missile weapon systems.