The production of ethanol and methane from corn stover (CS) was investigated in a biorefinery process. Initially, a novel soaking pretreatment (NaOH and aqueous-ammonia) for CS was developed to remove lignin, swell the biomass, and improve enzymatic digestibility. Based on the sugar yield during enzymatic hydrolysis, the optimal pretreatment conditions were 1 % NaOH + 8 % NH4OH, 50A degrees C, 48 h, with a solid-to-liquid ratio 1:10. The results demonstrated that soaking pretreatment removed 63.6 % lignin while reserving most of the carbohydrates. After enzymatic hydrolysis, the yields of glucose and xylose were 78.5 % and 69.3 %, respectively. The simultaneous saccharification and fermentation of pretreated CS using Pichia stipitis resulted in an ethanol concentration of 36.1 g/L, corresponding only to 63.3 % of the theoretical maximum. In order to simplify the process and reduce the capital cost, the liquid fraction of the pretreatment was used to re-soak new CS. For methane production, the re-soaked CS and the residues of SSF were anaerobically digested for 120 days. Fifteen grams CS were converted to 1.9 g of ethanol and 1337.3 mL of methane in the entire process.