In this study, an automatic take-off and landing system (ATOLS) based on radar guidance was developed to provide day/night, all weather, automatic takeoff and landing for unmanned aerial vehicles (UAVs). The ATOLS contains a ground-based tracking radar subsystem and an airborne transponder subsystem. This X-band tracking radar can provide precise position information for UAV-control operations (transponder mode) and fire-control systems (skin mode). It provides 360 degrees of azimuth coverage and therefore can be employed for navigation applications. Its maximum tracking range is about 17 km and accuracy of altitude measurement is about 1 ft with a 50-ft decision height above ground level. To substantiate the proposed ATOLS system, a differential global positioning system (DGPS) was also developed. When a UAV at a low-elevation angle is detected and tracked by a tracking radar, multipath propagation often leads to the degradation of tracking accuracy or even cause the radar to break track. As a result, it becomes a potential risk to flight safety of the ATOLS guidance and control of UAVs. To overcome this technical difficulty, this paper proposes a solution based on optimization of radar parameters to mitigate the interference from multipath signals. The feasibility of proposed method has been experimentally proven through the flight trials of UAVs. Compared to the conventional low-elevation tracking techniques, the proposed one employs the radar signal processing, and does not consume additional hardware and resources.