In this work, Lewis acids (FeCl₃, AlCl₃) and bases (Na₂CO₃, Na₂SO₃) were incorporated into a neutral deep eutectic solvent (DES, choline chloride/glycerin) to intensify the lignocellulose fractionation. The efficiency of fractionation in terms of the maximum delignification rate (89.7 %) and well-pleasing cellulose saccharification (100 %) could be achieved by the Lewis acid-mediated DES. An in-depth insight of the evolution of lignin structure revealed that Lewis acid-mediated DES could cleave the β-O-4 linkages efficiently to achieve a high yield lignin fragments. Meanwhile, the lignin fragments with the enhanced amphiphilic properties facilitate the preparation of lignin nanospheres (LNSs) via the self-assembly process. The resultant LNSs extracted by Lewis acid-mediated DES exhibited an excellent thermal stability, and enhanced antibacterial capacity, which were associated with the phenolic OH content. However, the extracted lignin by Lewis base-mediated DES was mainly attributed to the cleavage of lignin-carbohydrate complexes bond, especially the lignin-carbohydrate ester bond, which retained more ether bonds and a relatively complete structure. This study illuminated the different mechanisms of lignin extraction and the structural evolution of lignin from Lewis acid/base-mediated DES, and provided guidance to select suitable fractionation techniques for upgrading the downstream products.