This study conducted an in-depth investigation of the tracking controller of an aerial autonomous docking and landing trajectory system. To examine the system’s overall design, a dual-machine trajectory-tracking control simulation platform was created via MATLAB Simulink. Then, an autonomous docking and landing trajectory-tracking controller based on backpropagation proportional–integral–derivative control was designed, which fulfilled the trajectory-tracking control requirements in the autonomous docking and landing process by efficiently suppressing the external airflow disturbance according to the simulation results. A YOLOv3-based vision pilot system was designed to calibrate the rate of the aerial docking and landing position to eight frame per second. The feasibility of the multi-rotor aerial autonomous docking and landing system was verified using prototype flight tests during the day and at night.