Urban morphological change impacts the land surface temperature (LST) through modifying the net radiation, convective heat transfer, evapotranspiration, and heat storage on the ground. It is essential to quantify the contributions of these physical changes on LST changes. In this work, we conduct simulations using a weather research and forecasting model for the Chengdu–Chongqing urban agglomeration to identify causes of LST changes due to urban morphological changes through different morphological parameters: the aspect ratio, building plan area fraction, and average building height. A new method is proposed and used to quantify the contribution of these physical changes on LST changes. The results show as the aspect ratio increases, an increase of the average LST is induced by variations in radiation, and daytime cooling and nighttime warming are induced by variations in heat storage. There is warming associated with an increase in the building plan area fraction, which is mostly caused by a decrease in the efficiency of the long‐wave radiant heat emitted from the surface to the atmosphere. We also find that an increase in the average building height enhance the efficiency of convective heat transfer, which results in cooling. These results are important for the management of urban thermal environments.