Rapid urban development has changed urban substrate conditions, greatly affecting urban ecology and heating urban environment. Mitigating urban temperature rises by optimizing urban morphology is considered a promising approach; most studies ignore spatial and temporal heterogeneity. This study analyzes how plot spatial form influences urban thermal environment in the main Nanjing area from 2001, 2006, 2011, 2016, and 2021, based on geographically weighted regression models (spatio-temporal- and multi-scale). Results show that: 1. The formation of geothermal heat islands matches the direction of urban expansion, mainly due to changes in land substrate; 2. the spatio-temporal model performs best, indicating that urban morphology and surface thermal environment have obvious spatio-temporal heterogeneity; obvious scale differences exist in each index influencing the heat island effect; and 3. floor area ratio (FAR) and building density (BD) negatively and positively correlate with surface thermal conditions, with gradually increasing effect, respectively. Normalized difference vegetation index (NDVI) and distance from the nearest water body (Dis_W) negatively and positively correlate with surface thermal conditions separately; good ecological infrastructure reduces surface temperatures but shows a gradually weakening effect. Proximity to roads is associated with warmer thermal environment. This study elucidates how urban form influences surface thermal environments and suggests measures to reduce surface temperatures in the main urban Nanjing area.