With the continuous advancement of urbanization, the impervious surface expands. Urbanization has changed the structure of the natural land surface and led to the intensification of the urban heat island (UHI) effect. This will affect the surface runoff temperature, which, in turn, will affect the surface water temperature of urban lakes. This study will use UAS TIR (un-manned aerial system thermal infrared radiance) remote sensing and in situ observation technology to monitor the urban space surface temperature and thermal runoff in Kunming, Yunnan, in summer; explore the feasibility of UAS TIR remote sensing to continuously observe urban surface temperature during day and night; and analyze thermal runoff pollution. The results of the study show that the difference between UAS TIR LSTs and in situ LSTs (in situ air temperature 10 cm above the ground.) varies with the type of land covers. Urban surface thermal runoff has varying degrees of impact on water bodies. Based on the influence of physical factors such as vegetation and buildings and meteorological factors such as solar radiation, the RMSE between UAS LSTs and in situ LSTs varies from 1 to 5 °C. Land cover types such as pervious bricks, asphalt, and cement usually show higher RMSE values. Before and after rainfall, the in situ data of the lake surface water temperature (LSWT) showed a phenomenon of first falling and then rising. The linear regression analysis results show that the R2 of the daytime model is 0.92, which has high consistency; the average R2 at night is 0.38; the averages R2 before and after rainfall are 0.50 and 0.83, respectively; and the average RMSE is 1.94 °C. Observational data shows that thermal runoff quickly reaches thermal equilibrium with the land surface temperature about 30 min after rainfall. The thermal runoff around the lake has a certain warming effect on LSWT.