All vascular plants have lignin that interacts with polysaccharides in cell walls; however, the chemical structure of covalent lignin-carbohydrate (L-C) linkages remains unresolved because of the small number of L-C linkage relative to the polymer main chain. Sample isolation that predominantly maintains intact L-C linkages followed by advanced multi-dimensional NMR showed that the critical L-C linkage between lignin and xylan involves the α-position of the β-aryl ether unit of lignin and the sixth position of the glucuronic acid residue of 4-O-methyl glucuronoxylan. The L-C ester linkages occur primarily at the α-position of lignin, supporting a theoretical synthetic pathway through a quinone methide intermediate. In contrast, the conventional γ-L-C ester was undetectable, indicating that this linkage is not the primary type. Instead, the γ-acetyl-substituted lignin coexisted. The results on primary L-C linkages contribute to plant physiology and biology and advance research into biomass conversion.