Citric acid-based wood adhesive is considered a chemical-bonding wood adhesive. However, the detailed structures of the bonds between wood components and citric acid remain unknown. Here, we examine the chemical bonding structures between citric acid and wood by heteronuclear single quantum coherence-nuclear magnetic resonance (HSQC-NMR) analysis of wood-based molding using Japanese cedar (Cryptomeria japonica) and citric acid. In the HSQC-NMR spectrum of the wood molding, some esterified C/H correlation peaks appeared. The primary hydroxyl groups of polysaccharides, such as cellulose and galactoglucomannan, and the primary hydroxyl groups of the β-O-4 and β-5 substructures in lignin were found to be esterified with citric acid. In contrast, the secondary hydroxyl groups, except for xylan, barely reacted because of the steric hindrance. Additionally, the C/H correlation peak volumes of the reducing ends of mannan and xylan in the anomeric region increased after molding. It was clarified that the glycosidic bonds in the hemicelluloses were cleaved under the acidic molding condition with citric acid. The HSQC-NMR analysis revealed that the esterification of hemicellulose and lignin, and degradation of hemicellulose, proceeded under the molding condition. These results will promote understanding of the adhesive mechanism of citric acid-based wood adhesive and of the properties of the molding.