Here, a lactic acid/chlorine chloride-based deep eutectic solvent (DES) was used for the extraction of high-purity lignin (up to 94.7%) in high yield (up to 75%) from the hydrolysis/fermentation residue corn stover hydrolysate (CSH), which was generated from a pilot-plant-scale biorefinery. A range of extraction conditions were investigated, which involved varying reaction temperature, time, and DES composition. The relationship between lignin yield, purity, and structural characteristics with DES treatment conditions was determined. The extraction of high-purity lignin from hydrolysis/fermentation residues presents a promising approach for enhancing the economic feasibility of a lignocellulose biorefinery. It was also determined that DES extraction can produce lignin with a controlled range of molecular weight and functional group content.