We selected a typical developed city in east China, Nanjing, to evaluate the effect of recent national and local policies of air pollution control on emissions and air quality at city scale. Using a bottom-up methodology, the annual emissions of SO2, NOX, CO, NH3, primary fine particle matters (PM2.5), black carbon, and organic carbon were estimated to decline 70%, 22%, 49%, 72%, 64%, 65%, and 86%, respectively, while a slight increase was found for the non-methane volatile organic compounds (VOCs) during 2012–2016. The inter-annual change in NOX emissions was consistent with that in tropospheric NO2 column from satellite observation. Using air quality modeling (AQM), the city-scale emission inventory was further evaluated through comparisons between the simulated and observed concentrations of selected species. For SO2, NO2 and PM2.5, the normalized mean bias (NMB) and normalized mean errors (NMEs) for most cases were within 20% and 50% respectively, implying the reliability of the emission inventory. Regarding chemistry species, the modeling performance was better for sulfate and black carbon than nitrate and ammonium. From 2012 to 2016, the average of monthly PM2.5 concentrations for January, April, July, and October in Nanjing was found to decline 28% and 25% with AQM and ground observation, respectively, implying the benefit of emission control on aerosol pollution. Extra simulations with fixed emissions or meteorology conditions for 2012 and 2016 were conducted to understand the effects of emission control and meteorology variation on the reduced aerosol pollution.