Hydrothermal processes are vital for the aquatic ecology and environments of a river. In recent decades, as high dams have been increasingly built in large rivers, many channel-type reservoirs have formed. With a considerable amount of water being impounded, the original riverine hydrothermal regimes are modified or even profoundly changed. Existing studies are mainly focused on the thermal stratification in lake-type reservoirs with weak vertical mixing, while channel-type reservoirs are rarely investigated where the vertical mixing is relatively strong due to the large riverine discharge. In this study, the impact of dam operation on the Three Gorges Reservoir (TGR) was investigated, including the water level, discharge and temperature, by applying an integrated physics-based model developed using field data. The present numerical model was built based on a hydrothermal dynamic model and a box model. The results indicate that the reservoir has caused a significant thermal lag between the inflow and outflow, with the temperature difference being up to 5 °C. A highly correlated dependency has been found between the dam-regulated water level and the inflow/outflow temperature difference. The present method and conclusions are potentially useful for managing the TGR and other channel-type reservoirs.