Confocal Raman microscopy and confocal fluorescence microscopy were used to understand the mechanism of ionic liquid (IL) pretreatment of corn stover stem using 1-ethyl-3-methylimidazolium acetate. Three different cell types including tracheids, sclerenchyma cells and parenchyma cells were analyzed during IL pretreatment. We have established a direct correlation between changes in both the morphology and chemical composition of these plant cell walls during IL pretreatment as well as specific cell type information. It was observed that cell wall swelling occurs primarily in the secondary plant cell walls and the IL had little effect on compound middle lamella in terms of swelling. Accordingly, more significant cell wall swelling and distortion was observed in sclerenchyma cells and tracheids than in parenchyma cells, which contain primary plant cell walls. Lignin dissolution was faster in the secondary cell walls, while there was no preferential cellulose dissolution. Surprisingly, with a much thicker cell wall and a much higher original lignin content than parenchyma cells, tracheids showed much faster lignin and cellulose dissolution and cell wall swelling. Sclerenchyma cells showed an intermediate rate of lignin dissolution, while the cellulose dissolution rate and degree of cell wall swelling was comparable to that observed for tracheids. These results suggest that there is a synergistic mechanism of lignocellulose dissolution regarding cellulose and lignin dissolution and cell wall swelling that occurs during IL pretreatment. This study provides valuable new insights towards the mechanism of ionic liquid pretreatment and can potentially assist researchers in cell wall engineering for efficient cell wall deconstruction using ILs, and the methods established can be easily extended to other systems.