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Ice thickness has a significant effect on the physical and biogeochemical processes of a lake, and it is an integral focus of research in the field of ice engineering. The Qinghai–Tibetan Plateau, known as the Third Pole of the world, contains numerous lakes. Compared with some information, such as the area, water level, and ice phenology of its lakes, the ice thickness of these lakes remains poorly understood. In this study, we used an unmanned aerial vehicle (UAV) with a 400/900 MHz ice-penetrating radar to detect the ice thickness of Qinghai Lake and Gahai Lake. Two observation fields were established on the western side of Qinghai Lake and Gahai Lake in January 2019 and January 2021, respectively. Based on the in situ ice thickness and the propagation time of the radar, the accuracy of the ice thickness measurements of these two non-freshwater lakes was comprehensively assessed. The results indicate that pre-processed echo images from the UAV-borne ice-penetrating radar identified non-freshwater lake ice, and we were thus able to accurately calculate the propagation time of radar waves through the ice. The average dielectric constants of Qinghai Lake and Gahai Lake were 4.3 and 4.6, respectively. This means that the speed of the radar waves that propagated through the ice of the non-freshwater lake was lower than that of the radio waves that propagated through the freshwater lake. The antenna frequency of the radar also had an impact on the accuracy of ice thickness modeling. The RMSEs were 0.034 m using the 400 MHz radar and 0.010 m using the 900 MHz radar. The radar with a higher antenna frequency was shown to provide greater accuracy in ice thickness monitoring, but the control of the UAV's altitude and speed should be addressed. [ABSTRACT FROM AUTHOR]