The road transport sector in megacities is confronted with pressing local air pollution and carbon dioxide (CO₂) control issues. To determine effective policy instruments for saving energy and the co-control of air pollutants and CO₂, several mainstream measures were examined and compared in Chongqing's road transport sector from 2017 to 2035. An integration assessment framework was developed by combining the Long-range Energy Alternatives Planning (LEAP) system and a set of quantitative methods for evaluating the co-benefits of emission reductions (including the air pollutant equivalent (AP_eq), co-control coordinate system, and pollutant reduction cross-elasticity (Els_a/b)). Results showed that the shifting transportation modes scenario presented the most significant potential for energy-saving and emission reductions, reducing energy use by 30.9% and air pollutants and CO₂ emissions by approximately 27–32% compared with the business as usual (BAU) scenario in 2035. The improving energy efficiency scenario also provided significant co-benefits for reducing air pollutants and CO₂ emissions. Nevertheless, the promoting alternative fuel scenario may increase fine particulate matter (PM_2.5) emissions by 2.2% compared to BAU in 2035 under the cleanness of regional electricity in 2017. Our findings suggest that the shifting transportation modes were effective measures to reduce air pollutants and CO₂ in the short term synergistically, and highlighted the importance of cleaner electricity generation to develop electric vehicles in the medium and long term.