Background: Zhizhu pills (ZZP) are a traditional Chinese medicine (TCM) prescription, mainly used for clinically treating digestive diseases such as functional dyspepsia, constipation, and peptic ulcer. However, the chemical constituents of ZZP have rarely been reported. Objective: To establish an ultrahigh-performance liquid chromatography-quadrupole time of flight-mass spectrometry (UPLC-QTOF-MSE) method for the identification of chemical constituents in ZZP, including individual herbs and a complicated Chinese medicinal formula. Methods: The extracts of ZZP and its individual herb samples were analyzed by a UPLC-QTOF-MSE method on an ACQUITY UPLC HSS T3 column (100×2.1mmid, 1.8 lmparticle size) using a gradient elution of 0.1% formic acid in acetonitrile - 0.1% formic acid water (v/v) at a constant flow rate of 0.4 mL/min. With the MSE technique, both precursor ion and fragmentation information of compounds can be simultaneously acquired by alternating between low and high collision energy during a single chromatographic run. The data were analyzed on UNIFI. Results: A total of 154 compounds, including 67 flavonoids, 17 coumarins, 11 terpenoids, 10 alkaloids, six limonoids, six sequiterpene lactones, and 37 other components, were ultimately identified based on accurate masses and fragmentation patterns in ZZP and its individual herbs. Conclusions: This paper summarized fragmentation patterns of flavonoids, sequiterpene lactones, alkaloids, coumarins, and limonoids. A rapid, accurate, and comprehensive UPLC-QTOF-MSE method has been developed for the identification of chemical compounds and applied to simultaneously evaluate the quality and effectiveness of ZZP. Highlights: A total of 154 compounds were ultimately identified in ZZP and its individual herbs by UPLC-QTOF-MSE; the fragmentation patterns of flavonoids, sequiterpene lactones, alkaloids, coumarins, and limonoids in ZZP and its individual herbs are summarized. © The Author(s) 2022.