Choline chloride (ChCl)-based deep eutectic solvents (DESs) provide a tunable platform for lignocellulosic biomass fractionation; however, the relationship between DES molecular characteristics and delignification performance remains insufficiently understood. In this study, sugarcane bagasse was pretreated using six ChCl-based DESs, including ChCl–lactic acid (LacA), ChCl–levulinic acid (LevA), ChCl–ethylene glycol (EG), ChCl–glycerol (Gly), ChCl–urea (U), and ChCl–monoethanolamine (MEA), prepared at a molar ratio of 1:2. The pretreatment was conducted at 145 °C for 2 h using a DES/water system. Among the tested systems, ChCl–LevA exhibited the highest delignification efficiency, significantly enhancing cellulose accessibility and achieving the highest enzymatic glucose yield (66.49%). Structural analyses revealed that acidic DESs promoted β-O-4 bond cleavage and increased phenolic hydroxyl generation in regenerated lignin, resulting in excellent antioxidant activity. Correlation analysis demonstrated that lignin removal was strongly associated with the hydrogen-bond donating ability (α) and net hydrogen-bond acidity (α–β) of DESs. Density functional theory calculations further confirmed that the hydrogen bond strength between ChCl and hydrogen bond donors contributed significantly to delignification efficiency. This work provides mechanistic insights for the rational design of ChCl-based DESs toward efficient biomass fractionation and lignin valorization.