In this study, wood samples extracted from the Taicang ancient ship, dating back to the Yuan Dynasty, were investigated to study the characteristics of waterlogged archaeological wood. The macroscopic characteristics and microscopic structures were used to identify the wood species. To assess the degree of degradation of the waterlogged archaeological wood, X-ray diffraction (XRD), nanoindentation (NI), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM) were used to compare the new and ancient wood samples from the same species. The microscopic structures of the samples were identified as Pinus massoniana. The XRD and nanoindentation results revealed that the crystallinity index of the cellulose decreased from 41.07% to 33.85%, the elastic modulus was reduced by 20.90%, and hardness was reduced by 55.6% compared with the new wood. The FTIR spectra revealed that biological deterioration occurred in the cellulose and hemicellulose, but there was no noticeable change in the lignin content. These results provide helpful information for the conservation and restoration of ancient ships.