In this study, the effect of residual lignin and its structural modification of pretreated sugarcane bagasse (SCB) on enzymatic hydrolysis and fermentation was comprehensively evaluated by alkali and alkaline hydrogen peroxide (AHP) pretreatment. It was found that the AHP pretreatment had a negative influence on lignin dissolution compared with alkali pretreatment accompanied by a relatively low NaOH concentration (≤1%, w/v). However, there was less significance of enzymatic hydrolysis efficiency between NaOH and AHP pretreatment with >1% NaOH loading due to a high lignin removal above 78%. In addition, PEG 6000-assisted pretreatment was also performed to stabilize the enzymatic activity and further promote enzymatic digestibility and fermentability. The highest ethanol concentration of 59.96 g/L (61.22%) was obtained with PEG 6000-assisted 1% NaOH pretreated SCB at 30% solid loading. The structural features of the residual lignin indicated that most of the side chain structures were oxidized and that some aryl-ether bonds were dissociated after the pretreatments, especially in alkali pretreatment. The reduction of molecular weight and the breaking of lignin substructures help to achieve a more effective yield of enzymatic hydrolysis and fermentation.