There is increasing interest in the application of ionic liquids for the pretreatment and fractionation of lignocelluloses. In this study, a series of functional acidic ionic liquids (ILs) with various heterocyclic organic cations were synthesized. Corn stalks were successfully fractionated into lignin, hemicelluloses, and cellulose when ultrasonically pretreated with ILs at 70 °C for 3 h, and subsequently treated with alkaline extraction. High yields of IL-isolated lignin (18.3% to 19.6%) and (8.3% to 14.6%) were obtained using ILs in the absence and presence of water, respectively. The yield of cellulose ranged from 40.0 to 77.0% from IL treatments, whereas the yield of hemicelluloses ranged from 1.1% to 17.3%. Enzymatic hydrolysis of the isolated cellulose residual produced 89.2% to 94.9% reducing sugar with 77.8% to 86.1% glucose, which corresponded to 80.5% to 91.4% enzymatic conversion of cellulose. Syringol and vanillin were found as the main lignin degradation products.