In order to solve the problem of multiple flight routes caused by the large number of waypoints in the process of executing multi-way missions, a method of selection for UAV waypoint-mission based on ant colony route planning algorithm is proposed. Introduce the principle of the algorithm, calculate the pheromone concentration of the information point, realize the algorithm by the conversion rule of the worker-ant’s waypoint and the modification rule of the pheromone concentration, and carry out the simulation and result analysis. The result shows that it can ensure the aircraft complete all missions in the shortest path. This improves the efficiency of UAV’s task execution, reduces the time loss of the control system, and facilitates the realization of the UAV formation flight system.