The search for renewable deep eutectic solvents (DESs) for efficient biomass pretreatment based on a closed-loop biorefinery is of great interest and importance. Herein, we reported three novel lignin-based DESs prepared by choline chloride (ChCl) and 3-(4-hydroxyphenyl)propionic acid (HPA), 3-(4-hydroxy-3-methoxyphenyl)propanoic acid (HMPA) and their combination for corn stover pretreatment. The effects of three lignin-based DESs pretreatments on the chemical compositions of raw material, structural features of lignin, and enzymatic digestibility of cellulose were comprehensively analyzed, among which ChCl/HPA DES exhibited superior pretreatment efficiency, affording 58% of delignification, 62% of hemicellulose removal, and 85% of glucose yield. A high abundance of p-coumaric acid in the regenerated and remaining lignin samples makes them a sustainable feedstock to produce hydrogen bond donors of ChCl/HPA DES, as demonstrated by the results from 2D HSQC NMR analysis and catalytic depolymerization of lignins. These results could be conducive to creating an integrated biorefinery strategy for biomass valorization. Mass balance analysis indicated 81% of cellulose, 90% of hemicellulose, and 91% of lignin components in corn stover could be collected after DES pretreatment. This contribution offers a novel and efficient pretreatment method for corn stover fractionation based on a closed-loop biorefinery.