The heterogeneous structure and characteristic variability of industrial lignin present key challenges that hinder its use in numerous advanced scenarios. Herein, we explore amino acid-derived deep eutectic solvents (AADESs) featuring diverse side chain structures (glycine, alanine, valine, lysine (Lys), and proline) and serving as reactive media for modifying alkali lignin. For the first time, quantum chemistry and molecular dynamics simulations were employed to demonstrate the formation mechanism of AADESs. Among all the considered systems, the Lys-based system proved to be the most stable system owing to its strong nucleophilicity. Unlike choline chloride-based DES, the strong nucleophilicity of Lys could induce nanocrystallization and targeted modification of α-OH to attach phenolic hydroxyl in lignin. Breaking the β-O-4 and β-β linkages within lignin increased the phenolic hydroxyl content of the lignin by up to ~50 %. Additionally, the -NH