Unmanned aerial vehicles (UAVs) received an unprecedented surge of people’s interest worldwide in recent years. This paper investigates the specific problem of cooperative mission planning for multiple UAVs on the battlefield from a hierarchical decision-making perspective. From the view of the actual mission planning issue, the two key problems to be solved in UAV collaborative mission planning are mission allocation and route planning. In this paper, both of these problems are taken into account via a hierarchical decision-making model. Firstly, we use a target clustering algorithm to divide the original targets into target subgroups, where each target subgroup contains multiple targets. Secondly, a fuzzy ant colony algorithm is used to calculate the global path between target subgroups for a single-target group. Thirdly, a fuzzy ant colony algorithm is also used to calculate the local path between multiple targets for a single-target subgroup. After three levels of decision-making, the complete path for multiple UAVs can be obtained. In order to improve the efficiency of a collaborative task between different types of UAVs, a cooperative communication strategy is developed, which can reduce the number of UAVs performing tasks. Finally, experimental results demonstrate the effectiveness of the proposed cooperative mission planning and cooperative communication strategy for multiple UAVs.