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Global warming and increasing concentration of atmospheric greenhouse gas (GHG) have prompted considerable interest in the potential role of energy plant biomass. Cassava-based fuel ethanol is one of the most important bioenergy and has attracted much attention in both developed and developing countries. However, the development of cassava-based fuel ethanol is still faced with many uncertainties, including raw material supply, net energy potential, and carbon emission mitigation potential. Thus, an accurate estimation of these issues is urgently needed. This study provides an approach to estimate energy saving and carbon emission mitigation potentials of cassava-based fuel ethanol through LCA (life cycle assessment) coupled with a biogeochemical process modelGEPIC (GIS-based environmental policy integrated climate) model. The results indicate that the total potential of cassava yield on marginal land in China is 52.51 million t; the energy ratio value varies from 0.07 to 1.44, and the net energy surplus of cassava-based fuel ethanol in China is 92,920.58 million MJ. The total carbon emission mitigation from cassava-based fuel ethanol in China is 4593.89 million kgC. Guangxi, Guangdong, and Fujian are identified as target regions for large-scale development of cassava-based fuel ethanol industry. These results can provide an operational approach and fundamental data for scientific research and energy planning.