Abstract: In this study, the flow injection (FI) technology combined with the unique step wise multiple ions monitoring scanning (step-wise MIM) mode of Qtrap-MS was first established for the identification and discrimination of eight Murraya species. It only takes 5 min for each sample to detect approximate 600 compounds. The characteristic MS chromatograms of eight Murraya plants were analyzed by Analyst and SIMCA-P. The results of PCA showed that sect. Murraya and sect. Bergera were clearly divided into two categories, suggesting that there is difference in the chemical compositions between these two groups. Further detail analysis of the MS data could realize the preliminary structure elucidation of the component types contained in different plants. The main components in M. exotica and M. alata are coumarins, and polymethoxyflavones are rich in M. paniculata, while carbazole alkaloids are the major ones in sect. Bergera plants. The results are consistent with our previous comprehensive analysis of the chemical components of Murraya species. In conclusion, our research confirmed that FI-Qtrap-MS technology can be used for rapid identification and differentiation of similar plant species, providing reference for chemical taxonomy and a new method for the quality evaluation of medicinal materials.