To evaluate delignification as a pre-treatment for manufacturing processes, the chemical structure and composition of constituent polymers of Japanese cypress (Chamaecyparis obtusa) after chemical treatments (oxidation, solvent extraction, and alcoholysis) were investigated using a combination of attenuated total reflection infrared spectroscopy and 13C cross-polarization (CP)/ magic angle spinning (MAS) nuclear magnetic resonance (NMR) methods. Oxidation by the Klaudiz method selectively removed lignin despite a small weight loss (∼ 3.8%) because the active site of the reaction was at the terminal end of lignin. However, solvent extraction (dimethyl sulfoxide, ionic liquid, and dioxane) and alcoholysis simultaneously removed lignin and hemicellulose because the active sites of the reaction were at the interface between the lignin and hemicellulose, and the selectivity of the removed components was low. The effects of the reaction temperature and addition of acid were significant for chemical treatment, particularly for alcoholysis with acid (weight loss: from 1.7 to 52%), which removed most of the hemicellulose and lignin, resulting in increased cellulose crystallinity (13C CP/MAS crystalline/amorphous ratio: from 1.27 to 1.58). The removal of hemicellulose during lignification decreased the hydrophilicity, as evaluated by 1H MAS NMR, and increased the 1H spin-lattice relaxation time (T1H), revealing the higher affinity of hemicellulose for water. The 1H signal intensity was reduced to 0.62 in the dimethyl sulfoxide extraction at 150 °C compared to the untreated sample, and the T1H value increased to 1.6 s in the dioxane extraction with acid compared to 1.2 s in the untreated sample. Thermogravimetric and dynamic mechanical analyses indicated that the change in thermal behavior at lower temperatures required selectivity for delignification unless a significant amount of the hemicellulose was removed, such as during alcoholysis, where the acid demonstrated a lower maximum thermal decomposition temperature (329 °C). In actual manufacturing processes, these delignification methods should be used depending on the desired processing temperature.