AbstractTo reveal the structural changes of lignin during the soda–AQ cooking process and chemical bonds between lignin and xylan of wheat straw, 13C isotope-labeled technology was used in this study. First, 13C isotope-labeled xylose was injected into the living wheat straw. The success of 13C isotope-labeling was confirmed by the results of 13C abundance determination. Then, milled wood lignin-13C was extracted from wheat straw. The wheat straw, which had already been labeled by xylose-13C, was cooked by the soda-AQ process. Soda-AQ Lignin-13C and Residual Lignin-13C were extracted from black liquor and residual pulp. FT-IR, 13C-NMR, and 2D HSQC NMR analyses indicated that all lignin preparations were HGS-type lignin. The main lignin linkages were β-O-4’ units, β-β’ units, β-5’ units, and β-1 units, with the highest content of β-O-4’. Furthermore, 82.8% of β-O-4’ units, 77.2% of β-β’ units, 75.4% of β-5’ units, and 75.4% of β-1 units were degraded during the cooking process. LC bonds between lignin and xylan were at C2 and C5 positions of xylan. It was found that the C-2 position of xylan in wheat straw could be mainly connected to lignin by γ-ester bonds, and C-5 position of xylan in wheat straw was possibly linked with lignin by benzyl ether bonds.