Gardeniae Fructus, the dry fruit of Gardenia jasminoides Ellis, has been widely used for the treatment of different diseases. Although four types of processed Gardeniae Fructus products, characterized by differing effects, are available for clinical use, little is known regarding the respective processing mechanisms. In this study, ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry combined with multivariate statistical analysis was applied to characterize the chemical profiles of the differently processed Gardeniae Fructus products and to determine differences in their chemical compositions, thereby enabling us to identify those active compounds associated with the observed clinical effects. A total of 125 compounds were accordingly identified, among which, 56 were established as primary contributors to the significant differences (P < 0.01) between crude and processed Gardeniae Fructus, based on t-test analysis. Furthermore, the potential mechanisms underlying the chemical transformations that occurred during processing were discussed. The findings of this study may not only contribute to the more effective quality control of Gardeniae Fructus but also provide basic information for elucidating the mechanisms underlying the changes in chemical constituents in response to processing, and provide a basis for further investigations of Gardeniae Fructus processing mechanisms.

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