Lignin structure is an essential influence on the high-value application of agricultural waste, and it is crucial to investigate its structure and content. This study established a method for rapidly characterizing lignin structural units and interunit linkages content distribution using non-uniform sampling (NUS) technology in conjunction with two-dimensional heteronuclear single quantum coherence nuclear magnetic resonance (2D HSQC NMR). A green, high-yield tobacco lignin was isolated using a deep eutectic solvent (DES). Subsequent analysis revealed structural and content distribution differences in the lignin of the tobacco root, stalk, stem, and leaf parts. The results demonstrate that the 25 % NUS/2D HSQC NMR method is more effective than the conventional 2D HSQC NMR method regarding resolution, NMR experiment time, and the quantity of structural information obtained. It can reduce the NMR experiment time by more than fivefold, and the relative error is less than 2 %. The impact of three distinct DESs, namely choline chloride/oxalic acid/ethylene glycol, choline chloride/oxalic acid/gamma-valerolactone, and choline chloride/ethylene glycol/gamma-valerolactone solvents, on the isolate of tobacco lignin was evaluated. Choline chloride/oxalic acid/gamma-valerolactone proved the most effective for lignin isolation. Tobacco lignin consists of syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H) units, with ferulic acids (FA) also detected. G units are the main units in tobacco lignin, and the (3-O-4 linkages show the highest relative content. The NUS/ 2D HSQC NMR method established in this study has achieved rapid and accurate characterization of lignin structure, providing an efficient lignin structure analysis tool for applying agricultural waste value-adding.