In order to investigate the decay mechanism in red oak (Quercus rubra) and Schima (Schima spp.) wood in the ancient building of Xichuan Guild Hall, the changes in chemical composition were determined using Fourier-Transform Infrared Spectroscopy. The results were as follows: (1) The absorption peak intensities that represented the structural contribution of carbohydrates, and the crystallinity index of the cellulose in the red oak components, decreased noticeably by 55.70 percent in H1039/H1508, and 26.85 percent in H1370/H2900; while those of lignin were increased as a result of the brown rot process. These changes indicated that the brown-rot fungi had stronger degradation effects on hemicellulose and cellulose over lignin. (2) The absorption peak intensities of the carbohydrates (a part of the lignin) and the crystallinity index of the cellulose decreased noticeably by 22.50 percent in H1039/H1508, 25.00 percent in H1508/H1735, and 21.74 percent in H1429/H897 after white rot in the Schima wood components. These findings indicated that not only cellulose and hemicellulose but also lignin were attacked by white-rot fungi. By comparison, the extent of fungal damage in the wood components was lower in the Schima wood components than that in the red oak components.