Abstract In order to reduce air and soil pollution caused by open-field burning of stover and improve energy utilization efficiency in rural areas, Chinese government has provided many incentives for bio-energy utilization. But the amount of subsidy was not pegged to the actual environmental benefits of different energy utilization ways of agricultural waste. In this study, processed based life cycle assessment (LCA) method is used to investigate and compare the environmental impacts of three most common stover utilization ways, including biogas, stover pellets and stover gasification. The inventory analysis results are assessed by ReCiPe mid-point (H) method and end-point (H) damage evaluation, respectively. Based on the uncertainty analysis with Monte Carlo method, the compared results are expressed in probability and discussed, which shows the stover gasification utilization has more damage on the environment. Compared with the utilization of stover biogas, the utilization of stover pellets has less damage on resource depletion, but it is more harmful to human health and ecosystem. The materials used, transportation, equipment operation energy consumption, and stover utilization efficiency are found as the main parameters that affect the LCA results.