CO2 and SO2, while having different environmental impacts, are both linked to the burning of fossil fuels. Research on joint patterns of CO2 emissions and SO2 emissions may provide useful information for decision-makers to reduce these emissions effectively. This study analyzes both CO2 emissions and SO2 emissions embodied in interprovincial trade in 2007 and 2010 using multi-regional input–output analysis. Backward and forward linkage analysis shows that Production and Supply of Electric Power and Steam, Non-metal Mineral Products, and Metal Smelting and Pressing are key sectors for mitigating SO2 and CO2 emissions along the national supply chain. The total SO2 emissions and CO2 emissions of these sectors accounted for 81% and 76% of the total national SO2 emissions and CO2 emissions, respectively.