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Urban heat islands (UHIs) are caused by a multitude of changes induced by urbanization. However, the relative importance of biophysical and atmospheric factors in controlling the UHI intensity remains elusive. In this study, we quantify the magnitude of surface UHIs (SUHIs), or surface urban cool islands (SUCIs), and elucidate their biophysical and atmospheric drivers on the basis of observational data collected from one urban site and two rural grassland sites in and near the city of Nanjing, China. Results show that during the daytime a strong SUCI effect is observed when the short grassland site is used as the reference site whereas a moderate SUHI effect is observed when the tall grassland is used as the reference site. We find that the former is mostly caused by the lower aerodynamic resistance for convective heat transfer at the urban site and the latter is primarily caused by the higher surface resistance for evapotranspiration at the urban site. At night, SUHIs are observed when either the short or the tall grassland site is used as the reference site and are predominantly caused by the stronger release of heat storage at the urban site. In general, the magnitude of SUHI is much weaker, and even becomes SUCI during daytime, with the short grassland site being the reference site because of its larger aerodynamic resistance. The study highlights that the magnitude of SUHIs and SUCIs is mostly controlled by urban–rural differences of biophysical factors, with urban–rural differences of atmospheric conditions playing a minor role. [ABSTRACT FROM AUTHOR]