Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C–1H NMR correlation spectroscopy, via an heteronuclear single quantum coherence experiment, revealed substantial lignin β-aryl ether cleavage, deacetylation via cleavage of the natural acetates at the 2-O- and 3-O-positions of xylan, and uronic acid depletion via cleavage of the (1 → 2)-linked 4-O-methyl-α-d-glucuronic acid of xylan. In the polysaccharide anomeric region, decreases in the minor β-d-mannopyranosyl, and α-l-arabinofuranosyl units were observed in the NMR spectra from hydrothermally pretreated wheat straw. The aromatic region indicated only minor changes to the aromatic structures during the process (e.g., further deacylation revealed by the depletion in ferulate and p-coumarate structures). Supplementary chemical analyses showed that the hydrothermal pretreatment increased the cellulose and lignin concentration with partial removal of extractives and hemicelluloses. The subsequent enzymatic hydrolysis incurred further deacetylation of the xylan, leaving approximately 10 % of acetate intact based on the weight of original wheat straw.