Convenient detection method for bioactive food compounds and their metabolites in biological samples are needed to better understand their mechanism of actions. Herein, we developed a novel approach to directly monitor and visualize the distribution of 5, 3', 4'-tridemethylnobiletin (THN), a unique polymethoxyflavone metabolite derived from citrus polymethoxyflavone, in biological samples such as cultured cells and mouse colonic tissues. Our results showed that fluorescent conjugate could be formed between THN and 2-Aminoethyl diphenyl borate (DPBA) under simple reaction conditions, which was confirmed by both Raman spectroscopy and mass spectroscopy. We further demonstrated the application of DPBA-based conjugation reaction in the characterization of THN in different biological samples including floating cells, adherent cells, and animal tissues. This is the first report demonstrating direct fluorescent detection of polymethoxyflavone in biological samples.