Lignocellulosic biomass consists of cellulose, hemicelluloses, and lignin, which has different reactivity during chemical and physical pretreatment. This chapter discusses the impact of ionic liquids (IL) pretreatment on the major biomass components for the benefit of enzymatic conversion. It also discusses the technical and economic challenges of IL pretreatment. The toxicity of most of ILs remains unknown or undisclosed publicly. It has been reported that some ILs inhibit the subsequent enzymatic saccharification and fermentation. Certain ILs are highly efficient solvents or catalysts for biomass pretreatment to overcome the natural recalcitrance of lignocellulosic biomass contributed by cellulose crystallinity, the presence of lignin, functional groups on hemicelluloses, and interwoven linkages among these major components. The physical and chemical modifications of lignin and polysaccharides during pretreatment have a great impact on the following step of enzymatic hydrolysis, which includes enzyme loading, hydrolysis rate, enzymatic digestibility, and product recovery. The partial solubilization of the major components of biomass significantly increases enzyme accessibility and efficiency.