Intrusion detection is often used in scenarios such as airports and essential facilities. Based on UAVs equipped with optical payloads, intrusion detection from an aerial perspective can be realized. However, due to the limited field of view of the camera, it is difficult to achieve large-scale continuous tracking of intrusion targets. In this study, we proposed an intrusion target detection and tracking method based on the fusion of a 360° panoramic camera and a 3-axis gimbal, and designed a detection model covering five types of intrusion targets. During the research process, the multi-rotor UAV platform was built. Then, based on a field flight test, 3043 flight images taken by a 360° panoramic camera and a 3-axis gimbal in various environments were collected, and an intrusion data set was produced. Subsequently, considering the applicability of the YOLO model in intrusion target detection, this paper proposes an improved YOLOv5s-360ID model based on the original YOLOv5-s model. This model improved and optimized the anchor box of the YOLOv5-s model according to the characteristics of the intrusion target. It used the K-Means++ clustering algorithm to regain the anchor box that matches the small target detection task. It also introduced the EIoU loss function to replace the original CIoU loss function. The target bounding box regression loss function made the intrusion target detection model more efficient while ensuring high detection accuracy. The performance of the UAV platform was assessed using the detection model to complete the test flight verification in an actual scene. The experimental results showed that the mean average precision (mAP) of the YOLOv5s-360ID was 75.2%, which is better than the original YOLOv5-s model of 72.4%, and the real-time detection frame rate of the intrusion detection was 31 FPS, which validated the real-time performance of the detection model. The gimbal tracking control algorithm for intrusion targets is also validated. The experimental results demonstrate that the system can enhance intrusion targets’ detection and tracking range.