Promoting synergistic governance of CO2 emissions and air pollutant emissions reduction in the carbon market is crucial for China’s transition towards sustainable development. This study combines complete forward and backward linkages coefficients from input-output analysis with costeffective analysis to show how to enhance the synergistic effects of the national carbon market in CO2 emissions and air pollutant emissions reduction from a sectoral selection perspective and discuss the optimal sector inclusion sequence under different policy objectives using the 2020 non-competitive input-output table of 29 sectors. The results demonstrate that to enhance the synergistic effects of the national carbon market, sectors such as Coal Mining and Dressing, Oil and Gas Extraction, Petroleum and Coal Processing, Metal Smelting and Pressing, Electricity and Heat Production, as well as Transportation, should be included; sectors like Papermaking, Non-metallic Mineral Products, and Chemicals should not be included, which have low synergistic effects. The optimal sector inclusion sequence should be determined by combining different emission constraints.