Abstract To respond to the call of greenhouse gas emissions mitigation, an efficient carbon accounting framework should be proposed. Traditional narrowly defined estimation protocols that consider the direct emissions from native energy consumption may generally lead to underestimates of the carbon emissions derived from providing products and services. To comprehensively evaluate the supply-chain carbon performance in all economic sectors of China, the Economic Input–Output Life Cycle Assessment (EIO-LCA) based carbon footprint accounting framework should be employed. Because carbon emissions also occur in non-energy production processes, carbon emissions from the non-energy industrial process should also be incorporated into the accounting framework. This paper assessed 3 scopes of carbon emissions of Chinese economic sectors, including (1) direct emissions from energy consumption, and the industrial process, (2) emissions from purchased energy, (3) supply chain emissions combining both fuel combustion and industrial processes. The results shown that there is a huge underestimation of the carbon emission from various sectors using traditional carbon protocols compared with the tier 3 supply-chain CO2 emission. The emissions from industrial processes also constitute a large proportion, which cannot be ignored. In addition, we find that embodied CO2 emissions in exports concentrated on primary energy intensive sectors, indicating the importance of restructuring of export goods and services. It is proved that the three tier model provides a tool for decision makers to identify the national high carbon emission sectors and make effective carbon mitigation strategies.