Urban development has significantly modified the surface thermal environment in urban areas. This study provides the first attempt to characterize the urban development imprint on surface thermal environment for 323 cities across the entire country of China, using an intra-urban perspective. Specifically, it investigates the variation of surface thermal environment in terms of land surface temperature (LST) difference triggered by significant urban evolution of intra-urban division containing two primary classes: old urban areas developed by 1992 and new ones expanded in the 1992–2015 period. Under this “old-new” dichotomy, the relationship between urban development and the LST difference is explored through Multi-scale Geographically Weighted Regression (MGWR). Results reveal that urban development is closely related to the difference in LST between old and new urban areas in 2015, which varies from −2.66 °C to 2.46 °C, up to −6.27 °C in western China. 264 cities manifest relatively “cooler” urban environments in the generally larger-sized new urban areas. The seven selected urban development indicators can explain 75% of the variance in the LST difference through MGWR. Among them, the old-new elevation difference, the normalized difference vegetation index (NDVI) difference, and Gini coefficient are found to influence the LST difference in various spatially varying manners. The elevation difference, a generally underestimated nature-driven indicator, is found dominant in explaining the LST difference for 252 cities, among which 216 cities demonstrate higher LSTs in the urban areas with lower elevations. Overall, this study provides valuable information of human-environment interaction across many cities in a generalized way, which complements similar studies at local level, and helps to depict a complete picture of environmental impacts of urban development. The integrated workflow can also be promoted to other periods or other countries to examine the corresponding urbanization imprint on intra-urban surface warming.