This paper introduces a developed multi-sensor integrated system comprising a thermal infrared camera, an RGB camera, and a LiDAR sensor, mounted on a lightweight unmanned aerial vehicle (UAV). This system is applied to the inspection tasks of levee engineering, enabling the real-time, rapid, all-day, all-round, and non-contact acquisition of multi-source data for levee structures and their surrounding environments. Our aim is to address the inefficiencies, high costs, limited data diversity, and potential safety hazards associated with traditional methods, particularly concerning the structural safety of dam bodies. In the preprocessing stage of multi-source data, techniques such as thermal infrared data enhancement and multi-source data alignment are employed to enhance data quality and consistency. Subsequently, a multi-level approach to detecting and screening suspected risk areas is implemented, facilitating the rapid localization of potential hazard zones and assisting in assessing the urgency of addressing these concerns. The reliability of the developed multi-sensor equipment and the multi-level suspected hazard detection algorithm is validated through on-site levee engineering inspections conducted during flood disasters. The application reliably detects and locates suspected hazards, significantly reducing the time and resource costs associated with levee inspections. Moreover, it mitigates safety risks for personnel engaged in levee inspections. Therefore, this method provides reliable data support and technical services for levee inspection, hazard identification, flood control, and disaster reduction.