Driving co-abatement of Greenhouse Gas (GHGs) and Air Pollutants (APs) in the city level is crucial for fostering societal green and low-carbon transitions, yet comprehensive and refined researches at this level remain limited. To facilitate urban fine management of GHGs control and APs reduction, this study targeted nine categories of anthropogenic emission sources in Shanghai, a typical megacity of China, analyzing the co-benefits of three types of GHGs (CO2, CH4, N2O) and seven types of APs (SO2, NOx, CO, VOCs, NH3, PM2.5, PM10) via emissions flow, spatial distribution, hotspot regions identification, and scenario prediction. Results highlighted the source heterogeneity of different types and significant contributions of energy consumption. CO2 emissions showed a strong spatial correlation with SO2, NOx, and CO, followed by VOCs and PM. Hotspot regions for CO2-VOCs, CO2-NOx and CO2-SO2 co-abatement included power plants, petrochemical enterprises and chemical industrial parks in the southern coastal areas, iron and steel enterprises and power plants in the northern coastal areas, and airport areas in the central and eastern coastal areas, presenting great potential maximum reduction benefits. Achieving positive co-benefits in industrial sector would depend on the steady decline of CO2 emissions in power generation and steel industries. Introducing carbon capture devices and improving energy efficiency would be more beneficial to CO2 emission reduction, while increasing the share of clean energy and phasing out outdated vehicles, machinery, or production capacities are more effective in reducing APs. These mitigation measures could achieve 68.8 % and 47.6 % reduction for CO2 and APs by 2050, respectively, and the co-effect of CO2 and APs emission reduction would gradually increase with the continuous implementation of these measures.