Deep eutectic solvents (DESs) is a newly developed green solvent with low cost, easy preparation and regeneration. Because of its excellent solubility and swelling effect in lignocellulose, it has received widespread attention and recognition. In this study, choline-based deep eutectic solvents (DESs)—choline chloride-urea (CC-U), choline chloride-ethylene glycol (CC-EG), choline chloride-glycerol (CC-G), choline chloride-lactic acid (CC-LA), and choline chloride-oxalic acid (CC-OA)—were used to extract and separate bagasse. The effects of hydrogen bond donors on lignin separation and the fiber and lignin structure were investigated. All five DESs could dissolve lignin from bagasse; acidic DESs exhibited higher solubility than basic DESs. CC-OA effectively separated lignin and hemicellulose. CC-LA showed weaker lignin separation ability than CC-OA. CC-G, CC-EG, and CC-U were more inclined to selectively separate lignin than hemicellulose. The crystalline cellulose II structure was retained after DES pretreatment. Acidic DESs effectively improved the crystallinity of bagasse fiber; the crystallinities for CC-OA and CC-LA pretreatment were 62.26% and 61.65%, respectively. The lignin dissolved in DES was mainly syringyl lignin. The lignin dissolved in CC-U, CC-LA, and CC-OA contained a small amount of guaiacyl lignin.