Gleditsiae Spina, the thorn of Gleditsia sinensis Lam., has been used as an anti-inflammatory, anti-tumor, and anti-bacterial traditional medicine for hundreds of years in China. This study used high-performance liquid chromatography and tandem mass spectrometry combined with chemometric methods to allow the fast and accurate identification and quantification of the flavonoids compounds in Gleditsiae Spina, and created reliable criteria for accurate identification of Gleditsiae Spina and its adulterants. This research provides good evidence for the classification and quality evaluation of Gleditsiae Spina. Firstly, eight flavonoids compounds were detected and identified on the basis of their mass spectra, fragment characteristics, and comparison with published data. Then the mass spectroscopic fragmentation pathways of these compounds were determined and, in addition rutin, isoquercitrin, and quercitrin were detected in Gleditsiae Spina for the first time. The quantification was performed on a triple quadrupole tandem mass spectrometer in multi-reaction monitoring mode, and the baseline separation of the eight bioactive flavonoids components was achieved within 13 min. Furthermore, the proposed method was successfully applied for simultaneous quantitative determination of the eight Gleditsiae Spina compounds and adulterants obtained from different sources in China. Then, we built a classification model which showed a high level of accuracy predicting 100% of the samples, correctly.