Ancient wooden shipwrecks excavated from the marine environment are a significant part of cultural heritage. Investigating the degradation characteristics of waterlogged archaeological wood from shipwreck remains is not only crucial to study the mechanisms of wood decay in buried underwater environments, but also essential for the development of conservation techniques tailored to waterlogged wooden cultural relics. The degradation of waterlogged archaeological wood exhibits variability. This study focused on the waterlogged Dipterocarpus sp. wood remains from the archaeological excavation of the Xiaobaijiao Ⅰ, an ancient Chinese shipwreck. Internal and external sampling was conducted to explore the degradation characteristics. In this study, comprehensive characterization methodologies, including physical parameters analysis, optical microscopy (OM), polarized light microscopy (PLM), scanning electron microscopy (SEM), attenuated total reflectance-Fourier transform infrared spectrometry (ATR-FTIR), and dynamic vapor sorption (DVS) were employed to characterize the degradation differences between the internal and external parts of waterlogged archaeological wood. The results indicate that there was significant degradation difference between the internal and external parts of waterlogged archaeological wood, with the degraded areas clearly divided into the “outer layer” and “inner core”. The maximum water content (MWC) of the outer layer wood reached 687%, while the MWC of the inner core wood was 246%. The outer layer of wood was severely degraded, with the majority of the cells heavily decayed, and the birefringence of cellulose crystals having disappeared; furthermore, the secondary wall of the wood fibers exhibited a porous “spongy” structure, while only the middle lamella remained intact. The inner core wood was moderately degraded, with intact wood fiber cells coexisting with decayed cells, presenting the decay pattern of erosion bacteria. The FTIR results revealed that the residual chemical components in the cell walls of the outer layer of wood primarily consisted of lignin, while the inner core wood retained partial cellulose. The combination of FTIR spectrometry and principal component analysis (PCA) enabled accurate identification of severely and moderately degraded types. PCA loading curve analysis confirmed that cellulose was the main chemical component that distinguished the degradation difference between the outer layer and inner core wood. The hierarchical clustering analysis (HCA) of FTIR spectra identified the existence of a degradation transition zone between severely and moderately degraded wood. DVS analysis revealed the difference in moisture sorption properties between the outer layer and inner core wood. The Hailwood-Horrobin model was utilized to fit the sorption isotherms, allowing for the calculation of monolayer and multilayer adsorbed water contents in wood samples exhibiting various degrees of degradation. The results indicated that the equilibrium moisture content of the outer layer wood was higher than that of the inner core wood. This disparity was primarily attributed to the difference in the porous structure of the wood cell walls and cellulose content between the outer layer and inner core wood. Specifically, the porous cell wall structure of the outer layer of wood facilitates an increase in monolayer adsorbed water content, while the higher cellulose content in the inner core wood results in an elevation in multilayer adsorbed water content. This study employed a comprehensive analytical approach with innovations in sampling and FTIR analysis. Based on the positional differences in wood degradation, samples were collected from both the outer layer and inner core regions. By integrating chemometric analysis methods with FTIR spectrometry, the degree of wood degradation was rapidly determined on the basis of microscopic diagnosis, thereby enhancing the accuracy of assessing the preservation state of waterlogged archaeological wood. Furthermore, based on the investigation of microstructural and chemical components, the moisture sorption properties of wood cell walls at different degradation levels were characterized, and the influence of changes in cell wall structure on the hygroscopicity of waterlogged archaeological wood was further explored. This study revealed that the erosion bacteria were the main degraders for the Xiaobaijiao Ⅰ, and elucidated on the heterogeneous characteristics of degradation in shipwreck waterlogged archaeological wood, providing a perspective for understanding the mechanisms of wood decay in underwater burial environments.