The possibility of using biomass as a source of energy in reducing the greenhouse-effect imposed by carbon dioxide emission and relieving energy crisis is a matter of great interest, such as bioethanol production. Nevertheless, the cultivation of dedicated energy crops dose meet with some criticisms (conflict with food security and environmental degradation, for example). Nowadays sugarcane and cassava are regarded as the potential energy crops for bioethanol production. Endowed with natural resources and favorable weather condition, Yunnan province, China, is the major sugarcane and cassava production area in China. This paper presents production structures of these two crops in Yunnan and compares the sustainable production between the usages of sugarcane and cassava as bioethanol feedstock. Firstly, we estimated the technical efficiency for sugarcane and cassava production by adopting the production function and stochastic frontier production function. Field surveys from 61 sugarcane farmers and 50 cassava farmers were collected in June and September, 2008. Secondly, the sustainability of each crop production was evaluated. Since there is no generally accepted definition of sustainable production, a set of criteria was defined including 2 concerns (employment and food supply) from socio-economic area and 3 concerns (conversion rate to ethanol, water requirement, and fertilizer pollution) from environmental area. Empirical results demonstrated that the average production function was located below the frontier production function, 5% for sugarcane production and 7% for cassava production. These findings reflect the existence of technical inefficiency not only in the sugarcane production but also in the cassava production as well. But after considering sustainable production, cassava, which requires low agro-chemical, should be recommended as a prior energy crop in Yunnan with higher rates in ethanol conversion and dry matter.