In this study, based on the multi-source nature and humanities data of 270 Chinese cities from 2007 to2018, the spatio-temporal evolution characteristics of SO2 emissions are revealed by using Moran’s I, a hot spot analysis, kernel density, and standard deviation ellipse models. The spatial scale heterogeneity of influencing factors is explored by using the multiscale geographically weighted regression model to make the regression results more accurate and reliable. The results show that (1) SO2 emissions showed spatial clustering characteristics during the study period, decreased by 85.12% through pollution governance, and exhibited spatial heterogeneity of differentiation. (2) The spatial distribution direction of SO2 emissions’ standard deviation ellipse in cities was “northeast–southwest”. The gravity center of the SO2 emissions shifted to the northeast, from Zhumadian City to Zhoukou City in Henan Province. The results of hot spots showed a polarization trend of “clustering hot spots in the north and dispersing cold spots in the south”. (3) The MGWR model is more accurate than the OLS and classical GWR regressions. The different spatial bandwidths have a different effect on the identification of influencing factors. There were several main influencing factors on urban SO2 emissions: the regional innovation and entrepreneurship level, government intervention, and urban precipitation; important factors: population intensity, financial development, and foreign direct investment; secondary factors: industrial structure upgrading and road construction. Based on the above conclusions, this paper explores the spatial heterogeneity of urban SO2 emissions and their influencing factors, and provides empirical evidence and reference for the precise management of SO2 emission reduction in “one city, one policy”.