Abstract: OBJECTIVE To analysis alkaloids and their fragmentation behavior of Coptis rootlet by ultra performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry(UPLC-Q-TOF-MS). METHODS The separation was performed on the chromatographic column of Waters Acquity UPLC BEH C₁₈ by gradient elution with 0.1% formic acid water(A) and 0.1% formic acid acetonitrile(B). An electrospray ion source was used for mass spectrometry to collect data in both positive and negtive ion mode. Screening compounds in the Peakview 2.0/masterview 1.0 software based on the self-built Coptis chemistry database. The secondary spectra of more than 1 000 kinds of Chinese herbal medicine reference substances contained in Natural Products HR-MS/MS Spectral Library 1.0 software were analyzed by accurate mass number and comparison. RESULTS Nineteen alkaloids in Coptis rootlet were identified and inferred, and the fragmentation behavior of protoberberine, oxidized berberine and protopine alkaloids were analyzed. CONCLUSION This method provides a basis for the study of the constituents of Coptis rootlet, which proves the utilization of Coptis rootlet and lays a foundation for its further development and utilization.