This study takes the wooden components of the different parts of the ancient buildings at the site of the Zhuangzishang Conference as the object of study, and investigates the deterioration state of the different wood components. To assess their degree of degradation, the wood anatomy, basic density (BD), maximum water content (MWC), cell wall major components, X-ray diffraction (XRD), infrared spectroscopy (IR), and thermogravimetry (TG) were used to compare the samples of new and old wood from the same species. The window (W) was identified by microscopic characterization as cypress (Cupressus sp.), the footing beam (FB) and the weatherboard (WB) as pine (Pinus spp.), the purlin (P) and the column (C) as Chinses fir (Cunninghamia spp.), and the floor (F) as spruce (Picea sp.). In terms of their physical properties, the old wood had a lower basic density of 2.58%–38.19%, a lower air-dry density of 2.87%–39.81%, and a higher maximum moisture content of 8.52%–41.38% compared to the reference wood. The degradation of the FB, which has been subjected to moisture and sunlight, and the P, which has been subjected to termite damage, was greater than that of their conspecifics. The integrated holocellulose of the ancient wood was 3.34%–16.48% less, and the hemicellulose was 1.6%–21.92% less compared to that of the reference wood, and the lignin was 1.32%–25.07% more. The XRD results showed that the crystallinity of the cellulose was greater in the different species of ancient wood compared to the control wood, which was caused by the decrease in the amorphous zones of the hemicellulose and cellulose in the ancient wood. The IR indicated that the degradation of cellulose and hemicellulose occurred in the old wood of all species, from the new lignin uptake peaks in the UV-exposed W, FB, and WB compared to the control timber. The pyrolytic behavior of the ancient and control timber is mainly related to the degradation of the tree species and the ancient wood holocellulose. These results show that the differences in the wooden components of the different parts of the ancient buildings at the Zhuangzishang Conference site are mainly related to the species of trees used in the components, and are secondly related to the location of the ancient wood members, which provides useful information for the protection and repair of the ancient buildings at the site.