This study explored the role of VFAs and ethanol production on daily biogas and methane yield of sodium hydroxide (NaOH) pretreated corn stover (CS) in acidogenic and methanogenic phases during anaerobic digestion. The results from batch experiments revealed that the average methane and CO2 contents produced from NaOH pretreated CS were 53% and 38%, respectively. The concentration of VFAs and ethanol were over 17 g L-1 in the acidogenic phase, which were further converted into biogas in methanogenic phase. More specifically, the initially formed acetic, butyric and propionic acids were transformed into methane and CO2 in two different stages of methanogenic phase. On the other hand, two pretreatment regimes (NaOH pretreated CS and acidogenic effluent of NaOH pretreated CS) at the same organic loading rate were studied in continuously stirred tank reactors (CSTR). The methane and biogas yields obtained from acidogenic effluent of NaOH pretreated CS were 335 ml g.VS-1 and 548 ml g.VS-1; these values were 63.4% and 37.4%, respectively higher than the yields from NaOH pretreated CS sample. The results showed that sample from acidogenic effluent of NaOH pretreated CS improved methane production and maintained good system operation stability. (C) 2017 Published by Elsevier Ltd.