Lignin is an amorphous polymer that limits the enzymatic conversion of polysaccharides to fermentable sugars. Thus, a pretreatment that can enhance the accessibility of carbohydrates is a key step of successful biofuel conversion schemes. In this study, corn stover was fractioned into stem, cob, and leaf because their lignin is different. To elucidate the lignin changes, autohydrolysis, diluted acid, and alkali pretreatments were applied on the samples, followed by the isolation of cellulolytic enzyme lignin preparations. Alkaline nitrobenzene oxidation, 13C-Nuclear Magnetic Resonance (NMR), and 1H-13C heteronuclear single quantum coherence NMR were used to profile the lignin changes. The results indicated that corn stover lignin is a p-hydroxyphenyl-guaiacyl-syringyl-type lignin that incorporates p-coumarate and ferulate esters. The β-aryl-ether was the most abundant inter-unit linkage, followed by condensed linkages, e.g. pino-/syringaresinol, phenylcoumaran, and spirodienone. As for the non-pretreated samples, leaf lignin was more condensed than stem lignin and cob lignin. More lignin was removed by the alkali pretreatment due to more cleavage of β-aryl-ether linkages. As a comparison, more condensed linkages were generated by the acidic pretreatments. The decrease of the syringyl/guaiacyl ratio indicated that the residual lignin became more condensed and confirmed that guaiacyl and p-hydroxyphenyl units were more stable than syringyl units during the pretreatment.