Changes in the ultrastructure and chemical components, and their distribution in Japanese beech (Fagus crenata), during the ionic liquid 1-ethylpyridinium bromide ([EtPy][Br]) treatment were examined at the cellular level by light microscopy, scanning electron microscopy, and confocal Raman microscopy. Each of the tissues, including wood fibers, vessels and parenchyma cells treated with [EtPy][Br] showed specific morphological characteristics. Furthermore, lignin can be preferentially liquefied and eluted in [EtPy][Br] from the cell walls when compared to polysaccharides. However, the delignification was heterogeneous on the cell walls as lignin maintained a relatively high-concentration at the compound middle lamella, cell corners, inner surface of the secondary wall, and pits after [EtPy][Br] treatment.