Given rapid global urban development, increases to impervious surfaces, urban population growth, building construction, and energy consumption result in the urban heat island (UHI) phenomenon. However, the spatial extent of UHIs is not clearly mapped in many UHI studies based on a remote sensing approach. Therefore, we developed a method to extract the spatial extent of the UHI during the period from 2000 to 2021 in Nanjing, China, and explored the impact of urban two- and three-dimensional expansion on UHI spatial extent and UHI intensity. After cropland effects (i.e., bare soil) were eliminated, our proposed method combines the Getis-Ord-Gi* and the standard deviation of the normalized difference vegetation index (NDVI STD) to extract the UHI area from Landsat 5 and Landsat 8 images using land surface temperature (LST) spatial autocorrelation characteristics and the seasonal variation of vegetation. Our results show the following: (1) Bare farmland has a large influence on the extraction results of UHI—combined with the seasonal variation characteristics of NDVI STD, the impact of bare soil on UHI extraction was highly reduced, strongly improving the accuracy of UHI extraction. (2) The dynamics of the UHI area are consistent with the changes in the built-up area in Nanjing at both spatial and temporal scales, but with the increase of the urban green ratio, the UHI area of mature urban areas trends to decrease due to the cooling effect of green space. (3) The accumulation of population and GDP promote the vertical expansion of urban buildings. When the two-dimensional expansion of the city reaches saturation, the UHI intensity is primarily affected by three-dimensional urban expansion.