To achieve efficient utilization of compression wood (CW), a deeper insight into the molecular interactions is necessary. In particular, the role of lignin in the wood needs to be better understood, especially concerning how lignin contributes to its mechanical properties. For this reason, the properties of CW and normal wood (NW) from Chinese fir (Cunninghamia lanceolata) have been studied on a molecular scale by means of polarized Fourier transform infrared (FTIR) spectroscopy, under both static and dynamic loading conditions. Under static tensile loading, only molecular deformations of cellulose were observed in both CW and NW. No participation of lignin could be detected. In relation to the macroscopic strain, the molecular deformation of the cellulose C-O-C bond was greater in NW than in CW as a reflection of the higher microfibril angle and the lower load taken up by CW. Under dynamic deformation, a larger contribution of the lignin to stress transfer was detected in CW; the molecular deformation of the lignin being highly related to the amplitude of the applied stress. Correlation analysis indicated that there was a direct coupling between lignin and cellulose in CW, but there was no evidence of such a direct coupling in NW.