The water immersion of Pterocarpus wood produces strong blue fluorescence, which comes from the extract. The fluorescence contained in the extract is of interest for the identification of Pterocarpus wood. We conducted an investigation into the extraction solution of Pterocarpus wood and analyzed the mechanism of fluorescence in this species. Possible species of the fluorescent molecules are discussed based on the mixture. Liquid chromatography mass spectrometry (LC-MS) is used for an analysis of the extract, the obtained substances that may be fluorescent in Pterocarpus wood. In addition, the change in the fluorescence intensity with changes in the pH and concentration in the extract is also studied. The results show that the fluorescent molecule is quenched by aggregation (Aggregation-Caused Quenching; ACQ) and is unstable in over-acidic and over-alkaline conditions (especially acidic).