Termites are highly effective in lignocellulose degradation; however, the process of lignin deconstruction along the alimentary canal is not well understood. In this study, the wood metabolites in each gut segment were tentatively analyzed using pyrolysis-gas chromatography-mass spectrometry in the presence of tetramethylammonium hydroxide. Collectively, the significant differences in the pyrolysate distribution among each sample established (1) conservation of the major β-O-4' bonds of lignin during termite digestion, although a selective lignin substructure modification was observed across the whole gut; (2) initiation of lignin-polysaccharide dissociation, aliphatic oxidation/carboxylation, phenolic dehydroxylation in the foregut, and linkage modification of the 5-5', β-5', and β-1' substructures; (3) the continuation of foregut reactions into the midgut with further phenolic carboxylation/demethoxylation/carbonylation; and (4) phenolic/aliphatic esterifications in the hindgut. Overall, elucidation of the stepwise lignin unlocking mechanism in termites provides a valuable insight for understanding plant cell wall structure and its recalcitrance.