Structural changes of lignin from woody biomass during alkaline and acidic pulping conditions have been well documented in the literature. However, the subunit changes of lignin from corn stover during acid pretreatment have not yet been extensively explored. This study examined the impact of time (1-5 min) and temperature (140-190°C) of dilute acid (1% sulfuric acid w/w) corn stover pretreatment on sugar recovery and degradation product formation after pretreatment. Residual lignin samples from different pretreatment severities were isolated and subjected to 31P- NMR analysis. Cellulose hydrolysis performance, cellulose accessibility and chemical functional groups were also examined. With the increase in pretreatment severity, there is a gradual decrease in xylan content. In the mean time, the phenolic content of lignin, S/G/H ratio, condensed lignin units, and carboxyl units also changed significantly. There appears to be a strong correlation between changes of certain functional groups of lignin and enzyme digestibility. It is expected that the results would provide some critical insights on the impact of lignin degradation on enzyme digestibility and accessibility of the recalcitrant lignocellulosic substrates.