Ionic liquids (ILs) are widely used for biomass pretreatment because of their excellent dissolving capacity. The efficient and economical use of ILs in pretreatment greatly depends on revealing the underlying mechanism of biomass dissolution. Here, we observed that cellulose microfibrils of rice straw swelled in ILs using atomic force microscopy, and the swelling resulted in a decrease in cellulose crystallinity as determined by time-course X-ray diffraction analysis. The swelling of the IL-induced cellulose microfibrils greatly promoted the saccharification efficiency of rice straw. Compared with conventional acid or alkali solutions, strong hydrogen bond interactions between ILs of the appropriate size and polysaccharides resulted in cellulose microfibrils swelling in ILs, which was demonstrated by nuclear magnetic resonance and molecular simulation. Therefore, microfibril swelling is the key step in cellulose dissolution with ILs; effective swelling could accelerate cellulose dissolution and biomass pretreatment. Thus, those results are helpful in understanding the mechanism of lignocellulose dissolution in ILs and developing new ILs for biomass pretreatment.