The complex microstructure of lignocellulosic biomass restricts its conversion into bio-ethanol. In this study, the effects of an ionic liquid (IL) 1-allyl-3-methylimidazolium chloride ([Amim]Cl) pretreatment on the microstructure properties and cellulase hydrolysis efficiency of hybrid Pennisetum (P. americanum × P. purpureum, lignocellulosic biomass) were investigated. After the [Amim]Cl pretreatment, the bonds of lignin-carbohydrate complex (LCC) and C=O in xylan were destroyed and the content of inter-molecular H-bonds O(6)H…O(3’) decreased by 47.2%, while the content of intra-molecular H-bonds of O(2)H…O(6) and O(3)H…O(5) increased by 9.5% and 47.0%, respectively. The crystallinity and the crystallite size decreased by 20.8% and 42.22%, respectively, and the cellulose crystalline structure changed from cellulose crystalline I to cellulose crystalline II. The specific surface area increased from 0.15 to 10.11 m2/g after the [Amim]Cl pretreatment. The glucose recovery increased by 10.3 times after being pretreated with [Amim]Cl, compared with the unpretreated sample.