Rationale: Macleaya microcarpa (Maxim.) Fedde belongs to the genus Macleaya of the Papaveraceae family. Benzylisoquinoline alkaloids (BIAs) are considered the main bioactive constituents of M. microcarpa. Methods: Using high-performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry (HPLC/QTOFMS/MS) we identified BIAs in the aerial parts of M. microcarpa in the early flowering stage. Target profiling and identification of BIAs in the extracted samples from the fresh aerial parts of M. microcarpa were exclusively based on a personal, accurate, mass database of known compounds and the mass spectral fragmentation behavior of Macleaya alkaloids. Results: A total of 97 alkaloids, comprising 7 benzyltetrahydroisoquinolines, 1aporphine, 9 tetraprotoberberines, 3 protoberberines, 2 N-methyltetrahydroprotoberberines, 4 protopines, 47 dihydrobenzophenanthridines, and 24 benzophenanthridines, were identified from the fresh aerial parts of M. microcarpa, and 77 of these were detected for the first time in M. microcarpa. In addition, some of the screened alkaloids were related to the biosynthetic pathways of sanguinarine and chelerythrine. Conclusions: The integrated method is sensitive and reliable for screening and identifying trace or ultra-trace isoquinoline alkaloids and has contributed to a better understanding of BIAs in the fresh aerial parts of M. microcarpa. © 2019 John Wiley & Sons, Ltd.