When precipitation happens in summer, the thermal runoff from the impervious surface flows into the urban lakes, causing the rise of the surface water temperature. Such a process eventually leads to the short-term effects of cyanobacteria blooms in eutrophic lakes and the long-term effects of changes in the structure and quantity of lake species. It is of great scientific significance to understand the heat exchange process between surface air, underlying surface, and surface runoff and reveal the thermal runoff formation mechanism. In this study, the heat transfer models between land, surface-air, and surface-water were built, aiming to quantify the heating process of surface runoff caused by surface heat load under real conditions to clarify the heat exchange process. The results show that the two established models can accurately simulate the heat exchange process. Based on our model simulations and field measurements, we analyzed the impact of weather conditions, hydrological conditions, and underlying surface types on runoff temperature. The study finds that the initial surface temperature, wind speed, rainfall intensity, thermal conductivity, and the underlying surface’s water permeability can explain 95.4% and 91.9% of the change in a temperature difference of surface runoff and the change in runoff temperature increase rate, respectively. The initial surface temperature is the most critical factor in the heat exchange process. The reduction of urban ventilation will aggravate the heat effect of surface runoff. Compared with the underlying permeable surface, the impervious surface is the main driving force for the formation of surface thermal runoff pollution.