The recalcitrant nature of lignocelluloses requires a pretreatment process before the fermentative butanol production. The commonly used pretreatment processes, such as steam explosion, sulfuric acid, ammonia fiber explosion, ionic liquid (IL), and biological, require different quantities and types of process chemicals, and produce different quality and quantity of fermentable sugars. This study determines life-cycle greenhouse gas emissions (GHG) these pretreatment methods by developing a system-level process model including corn stover feedstock supply system and the downstream butanol production process. This study further evaluates the uncertainty associated with energy use and GHG emissions for each stage of the entire butanol production chain and provide the future optimization opportunities. Probabilistic results of these analyses describe a distribution of GHG emissions with an average of 18.09-1056.12 gCO2e/MJ and a 95% certainty to be less than 33.3-1888.3 gCO2e /MJ. The highest GHG emissions of IL-pretreatment of 1056.12 gCO2e/MJ reaches to 89.8 gCO2e/MJ by switching IL-recovery from 80 to 99 wt %, which is the most influential parameter for IL-pretreatment. Additionally, credits from excess electricity, butanol yield, nitrogen replacement, and diesel fuel for transportation and harvesting were the most influential parameters. Based on the current state of technologies, apart from ionic liquid and biological pretreatments, other pretreatment processes have similar metrics of sustainability.