Pesticide spray is a key session of management of fruit trees and air-assisted ground sprayers are commonly used in orchards. However, conventional equipment may lead to concerning issues, such as excessive chemical use and serious drifts. This study designed a target detecting and tracking system for an orchard spray robot, which was specifically developed for spraying onto middle and lower parts of fruit trees in terms of the background of stereo plant protection. The robot had an electric crawler chassis. A lifting implement and a spray bracket with nozzles were specifically designed. In terms of the control system, the system consisted of four main units: including a LiDAR detection unit, a height adjustment unit, an angle adjustment unit, and a control unit. For the LiDAR detection unit, RPLIDAR S1 was used to detect trees and measure the distance between the robot and the trees. For the height adjustment unit, a lifting implement combined with ranging finders was utilized to raise the height from the ground to the spray bracket, so that nozzles could reach the calculated height of target points in real-time. For the angle adjustment unit, electric pushrods with encoders were exploited to change the angle of the spray bracket, so that the nozzles could follow the calculated angle of target points. In terms of the control unit, STM32F429, a microcontroller, was applied. Based on the structure, three steps were developed for operation. First, general characteristics of fruit trees were analyzed based on the investigation in the orchards in Beijing, Shanxi, and Guangxi, and detection areas were determined based on these characteristics. Then, LiDAR was used to acquire the point clouds of canopies of the trees, and the polar distance and polar angle of target points were computed based on the maximum and minimum polar coordinate values of points of the trees. At last, the target points were obtained by the division and filtering of the point clouds in the areas, and the final distance and elevation angle of spraying were calculated based on these targets. Furthermore, the mathematical relations, one, between the elevation angle of the targets and the pulse number of the encoder, the other, between that and the stroke of pushrods, were established. Meanwhile, the measurement and control method of elevation angles of the spray bracket was designed. Incremental Proportion Integral Differential (PID) was applied for the angle variation so that elevation tracking could be achieved. To demonstrate the performance of the system, trials were conducted on the campus of China Agricultural University to acquire the data of Begonia canopies. The route of the robot was ‘U’ shaped and three trees were randomly selected for analysis. Results indicated that the system could adapt to different sizes and characteristics of canopies. Meanwhile, the targets of the three trees were concentrated on the height from 2.0 m to 3.5 m, which illustrates that the range could meet the requirement of spray onto middle and lower canopies of trees. Furthermore, the trials identified that the minimum spray elevation angle was 47.8°, while the maximum spray elevation angle was 51.4°. The maximum adjustment time of spray elevation angle between continuous targets was 0.06 s, which meant that the positioning of targets was fast. The system could offer a solid theoretical basis of the target following spray and the study could give a technical reference on chemical reduction, energy-saving, and drift decrease of plant protection in orchards.