In this study, we apply the inter-regional input–output model to explain the relationship between China’s inter-regional spillover of CO2 emissions and domestic supply chains for 2002 and 2007. Based on this model, we propose alternative indicators such as the trade in CO2 emissions, CO2 emissions in trade, regional trade balances, and comparative advantage of CO2 emissions. The empirical results not only reveal the nature and significance of inter-regional environmental spillover within China’s domestic regions but also demonstrate how CO2 emissions are created and distributed across regions via domestic production networks. The main finding shows that a region’s CO2 emissions depend on not only its intra-regional production technique, energy use efficiency but also its position and participation degree in domestic and global supply chains.