It is of great value to research the problem of forest pest and disease control. Currently, helicopters play an important role in dealing with this problem. However, the spraying route planning still depends on the pilot’s driving experience, which leads to low efficiency and less accurate coverage. For this reason, this paper attempts to use intelligent algorithms to plan the pesticide spraying route for helicopters. When the helicopter is conducting spraying operations in multiple forest areas, the routes are divided into two parts: pesticide spraying routes for individual forest areas and dispatch routes between multiple forest areas. First, the shorter spraying route with fewer turnarounds for individual forest areas was determined. Then a two-layer intelligent algorithm, a combination of a genetic algorithm (GA) and ant colony optimization algorithm (ACO), was designed to determine the dispatch route between multiple forest areas, which is referred to as GAACO-GA. The performance was evaluated in self-created multiple forest areas and compared with other two-layer intelligent algorithms. The results show that the GAACO-GA algorithm found the shortest dispatch route (5032.75 m), which was 5.60%, 5.45%, 6.54%, and 4.07% shorter than that of GA-GA algorithm, simulated annealing-GA (SA-GA) algorithm, ACO-GA algorithm, and particle swarm optimization-GA (PSO-GA) algorithm, respectively. A spraying experiment with a helicopter was conducted near Pigzui Mountain, Huai’an City, Jiangsu Province, China. It was found that the flight path obtained from the proposed algorithm was 5.43% shorter than that derived from a manual planning method. The dispatch route length was reduced by 16.93%, the number of turnarounds was reduced by 11 times, and the redundant coverage was reduced by 17.87%. Moreover, helicopter fuel consumption and pesticide consumption decreased by 10.56% and 5.43%, respectively. The proposed algorithm can shorten the application route, reduce the number of turnarounds and the cost of spraying operations, and has the potential for use in spraying operations in smart forestry and agriculture.