The impacts of ionic liquid and alkaline pretreatments on the enzymatic hydrolysis and thermal degradation of corn stover were investigated to better understand the mechanism of biomass pretreatment. Corn stover samples were pretreated at a 5 wt% biomass loading in 1-butyl-3-methylimidazolium acetate ([C4mim][OAc]) at different temperatures varying from 50 to 110 째C for 6 h. NaOH solutions of three different concentrations were used to pretreat the corn stover samples: 0.5 wt%, 1.0 wt% and 4.0 wt% at temperatures of 35 and 50 째C for 6 h. Different pretreatment conditions enabled various degrees of alteration to their structures. Structural factors which led to enhanced enzymatic digestibility and variations in thermal degradation behavior were compared and discussed. It was found that biomass pretreatment enhanced enzymatic digestibility of corn stover which was correlated with decrease in thermal degradation temperature and increased amount of materials degrading at lower temperatures. Pretreatment did not always lead to a decrease in activation energy of the thermal degradation of biomass samples. The activation energy was mainly influenced by cellulose crystallinity. XRD analysis also indicated that [C4mim][OAc] interacted with (101) and (10) lattice planes of cellulose during the initial dissolution process.