As a renewable biological macromolecule with aromatic structure, lignin can serve as matrix substance to maintain cell wall integrity and is regarded as the natural biomass recalcitrance. Substantial differences in the cell wall lignin topochemistry between opposite (Ow) and compression wood (Cw) trachieds in Pinus bungeana Zucc. were visualized during [Emim][OAc] pretreatment at room temperature. The ionic liqiuds treatment induced a more obvious wall swelling for highly lignified Cw tracheids than that of Ow, while dynamic Raman spectra analysis indicated the higher lignin and carbohydrates removal for Ow tracheids. Raman imaging further revealed that both lignin and carbohydrates were dissolved simultaneously within the middle lamella and secondary wall of Ow and pretreatment has little effects on Cw tracheids wall. Moreover, it was demonstrated that lignin composition was the key factor to affect the composition dissolution. In particular, lignin G-units were selectively removed from cell corner middle lamella (52.3 %) and secondary wall (62.0 %) of Ow tracheids. When cotton fiber, as a reference was treated under the same conditions, lattice conversion moving from cellulose I to II occurred. The findings confirmed the important role of lignin compostion in the dissolution behavior of carbohydrate dominant tracheids wall.