Current aerial plant protection with Unmanned Aerial Vehicles (UAV) usually applies full coverage route planning, which is challenging for plant protection operations in the orchards in South China. Because the fruit planting has the characteristics of dispersal and irregularity, full-coverage route spraying causes re-application as well as missed application, resulting in environmental pollution. Therefore, it is of great significance to plan an efficient, low-consumption and accurate plant protection route considering the flight characteristics of UAVs and orchard planting characteristics. This study proposes a plant protection route planning algorithm to solve the waypoint planning problem of UAV multi-objective tasks in orchard scenes. By improving the heuristic function in Ant Colony Optimization (ACO), the algorithm combines corner cost and distance cost for multi-objective node optimization. At the same time, a sorting optimization mechanism was introduced to speed up the iteration speed of the algorithm and avoid the influence of inferior paths on the optimal results. Finally, Multi-source Ant Colony Optimization (MS-ACO) was proposed after cleaning the nodes of the solution path. The simulation results of the three test fields show that compared with ACO, the path length optimization rate of MS-ACO are 3.89%, 4.6% and 2.86%, respectively, the optimization rate of total path angles are 21.94%, 45.06% and 55.94%, respectively, and the optimization rate of node numbers are 61.05%, 74.84% and 75.47%, respectively. MS-ACO can effectively reduce the corner cost and the number of nodes. The results of field experiments show that for each test field, MS-ACO has a significant optimization effect compared with ACO, with an optimization rate of energy consumption per meter of more than 30%, the optimization rate of flight time are 46.67%, 56% and 59.01%, respectively, and the optimization rate of corner angle are 50.76%, 61.78% and 71.1%, respectively. The feasibility and effectiveness of the algorithm were further verified. The algorithm proposed in this study can optimize the spraying path according to the position of each fruit tree and the flight characteristics of UAV, effectively reduce the energy consumption of UAV flight, improve the operating efficiency, and provide technical reference for the waypoint planning of plant protection UAV in the orchard scene.