This article discusses an integrated framework built to compute the cost of stover‐based E85, as well as its life cycle energy efficiency and CO2 emission, with consideration of uncertainties of the policy‐related factors, in China. Results show that co‐product treatment greatly influenced the performance of E85 route. The calculated values of energy efficiency in co‐product burning for electricity scenario (the base scenario) and that in co‐product for selling scenario (the alternative scenario) are 4.41 and 3.61, respectively. CO2 emission of the stover‐based route is 99.7% more than that of the gasoline route in the base scenario and 55.3% less than that of the gasoline in the alternative scenario. The costs of E85 in these two scenarios are 9.78 and 7.76yuan/L, respectively. Based on the sensitivity and uncertainty analysis, the article suggests the following: (1) stover‐based E85 is currently not competitive in terms of cost; (2) on the current stage, to make E85 competitive, policymakers should be concerned about stimulating processing innovation, providing subsidies on ethanol, feedstock and co‐product, as well as raising gasoline price, rather than increasing carbon tax rate/promoting Cleaner Development Mechanism (CDM) projects or influencing consumers’ Willingness to Pay (WTP) for E85.