Black soybean (Glycine max L.) is one of the most popular crops with various application in the world. Its seed coat contains various natural pigments compounds such as anthocyanin and flavonoid. In this study, we optimize the extraction conditions of eight polyphenols from whole of black soybean and seed coat, evaluate their extraction effect, and separation resolution at different pH-range. The multiple reaction monitoring (MRM) method was analyzed by using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) with simultaneous positive and negative electrospray ionization in a single analytical run. Eight polyphenols were separated within 9 minutes of run time with LC-MS/MS operated mode. The calibration graphs were linear over the concentration ranges of 0.01 to 1 mg/L for all polyphenol. Regression coefficients were in the range > 0.99. The limit of detection value, calculated from the blank tests based on 3σ, was 1 μg/L for all polyphenol. The RSD values corresponding to the intra-day and inter-day repeatability were lower than 11% and accuracies between 85-115%. It is shown that the modified solvent system that applied in LC-MS/MS detection could be developed as a useful tool for the study of water-soluble phenolic compounds.