Utilization of cell wall components of woody biomass has attracted attention as alternatives for fossil fuels towards a sustainable society. A semi-flow hydrothermal treatment was used to fractionate the beech (Fagus crenata) wood into cellulose-rich residues and lignin-rich precipitates. The enzymatic saccharification of the cellulose component in the residue was enhanced significantly because the preferential delignification from the secondary wall increased enzyme accessibility. Meanwhile, the precipitated lignin was soluble in organic solvent and exhibited clear photoluminescence (PL) according to the chromophore distances. Furthermore, the carbocation scavenger, 2-naphthol, was impregnated into the beech wood to inhibit the lignin re-condensation reaction. As a result, the digestibility of the cellulose component in the residue increased because unproductive enzymatic binding of lignin and lignin re-condensation were both suppressed. In addition, the PL intensity of the precipitates was significantly enhanced, indicating that 2-naphthol bound to the lignin molecules influenced the PL properties. Overall, fractionation using a semi-flow hydrothermal treatment efficiently uses both polysaccharides and lignin, especially the impregnation of 2-naphthol provided advantages for both saccharides and lignin. Monosaccharides can be converted into valuable products via a sugar platform, and the lignin precipitates exhibit useful PL properties that give them significant potential as a feedstock for numerous valuable materials, such as fluorescence reagents and spectral conversion agents. The results presented herein provide insights that are crucial for the comprehensive utilization of cell wall components for sustainable biorefinery systems.