A large number of archaeological wooden building poles have been excavated from the Hai Menkou site (Yunnan province, China). Lignin can be transformed and altered accompanied with significant loss of carbohydrates during this process. Elucidation of chemical and structural transformations of lignin is of primary importance for understanding both the nature of degradation processes and the structure of waterlogged archaeological wood, and crucial for developing proper consolidation technology and restoring artifacts of historical and cultural value. In this study, state-of-the-art analytical techniques, including SEM, FT-IR, XRD, CP-MAS C NMR, 2D-HSQC NMR, P-NMR, CRM, GPC and TG analysis, were all employed to elucidate the structural characteristics of lignin in waterlogged and reference Pinus wood. The results interpreted by NMR analysis demonstrated the depolymerization of lignin via cleavage of β-O-4, β-5, -OCH and some LCC linkages, leading to a higher amount of free phenol OH groups in the lignin from the ancient waterlogged wood as compared to that of the reference wood. Microscopically, it was found that extensive degradation of carbohydrates in cell walls was mainly occurred in secondary cell walls, while the lignin concentrations were relatively increased in CCML and S regions in the plant cell wall of the ancient wood.