AbstractSeveral representative ionic liquids (ILs) were synthesized, and [Emim]OAc was chosen as environment-friendly solvent for enzymatic in situ saccharification in view of its biocompatibility with both natural and microcrystalline cellulose, as well as its enzymatic activity. With the microwave pretreatment of natural and microcrystalline cellulose, directly enhancing the in situ enzymatic saccharification, the rate was compared versus an untreated control by the detection of dinitrosalicylic acid (DNS). It is suggested that the molecular structure of cellulose in the process of pretreatment was changed, e.g. intramolecular hydrogen bonds were broken (detected by FT-IR), and the crystallinity (monitored by SEM and XRD) changed significantly from a crystalline to an amorphous pattern. These changes of cellulose led to an increase of reducing sugar conversion during cellulose enzymatic hydrolysis.