The relationship between the cell wall ultrastructure of waterlogged wooden archeological artifacts and the state of water bound to cell walls and free in voids is fundamental to develop consolidating and drying technologies. Herein, a lacquer-wooden ware and a boat-coffin dating 4th century BC were selected as representative artifacts to study. Wood anatomy results indicated that they belonged to Idesia sp. and Machilus sp., respectively. They exhibited a typical spongy texture, as revealed by SEM observations, and their water contents had increased significantly. Solid state NMR, Py-GC/MS, imaging FTIR microscopy and 2D-XRD results demonstrated that the deterioration resulted from the partial cleavages of both polysaccharide backbones and cellulose hydrogen-bonding networks, almost complete elimination of acetyl side chains of hemicellulose, the partial depletion of β-O-4 interlinks, as well as oxidation and demethylation/demethoxylation of lignin. These further caused the disoriented arrangement of crystalline cellulose, and the decrease in cellulose crystallite dimensions and crystallinity. In consequence, mesopores and macropores formed, and the number of moisture-adsorbed sites and their accessibility increased. Moreover, results on free water deduced by the changes of pore structure and the maximum monolayer water capacity achieved by the GAB model indicated that water in waterlogged archeological wooden artifacts was mainly free water in mesopores.