Based on the panel data of 283 cities in China from 2009 to 2018, this paper analyzes the effect of urban green scientific and technological innovation enhancement on hazardous air pollutants using the GS2SLS method, which simultaneously controls for model endogeneity and spatial spillover effects and reveals the transmission mechanism of urban green scientific and technological innovation level. It was found that (1) There is a significant spatial spillover effect of hazardous air pollutants between regions, both in China as a whole and in the eastern, central, and western parts of the country, and the spatial spillover effect of hazardous air pollutants is significantly greater in the eastern and central parts of China than in the western parts. (2) Green technological innovation has a significant inhibitory effect on hazardous air pollutants in cities in eastern and central China. An extended study found that the improvement in green technology levels in innovative cities has a better effect on controlling hazardous air pollutants than in non-innovative cities. (3) The energy- saving and green economy effects have a mediating influence on the effect of green technological innovation on hazardous air pollutants in cities, and the simultaneous occurrence of these two effects in green technological innovation serves to enhance the transmission of hazardous air pollutants in order to facilitate the long-term management of haze.