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Quzhou Aurantii Fructus (QAF), the dried immature fruit of Citrus changshan-huyou Y.B. Chang, is similar to Aurantii Fructus (AF), the dried immature fruit of Citrus aurantium L. or its cultivars, in terms of composition, pharmacological action, and appearance. However, potential chemical markers to distinguish QAF from AF remain unknown owing to the lack of a comprehensive systematic chemical comparison aligned with discriminant analysis. To achieve a better understanding of the differences in their composition, this study aimed to identify the basic chemical compounds in QAF (n = 42) and AF (n = 8) using ultra-performance liquid chromatography coupled with electron spray ionization and quadrupole time-of-flight mass spectrometry (UPLC−QTOF/MS) and gas chromatography coupled with mass spectrometry (GC−MS). Principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS−DA), and hierarchical clustering analysis (HCA) were used to further analyze, screen, and verify potential chemical markers; the antioxidant capacity was assayed in vitro. A total of 108 compounds were found in QAF and AF, including 25 flavonoids, 8 limonoids, 2 coumarins, and 73 volatile components. The chemometric analysis indicated that the main components in QAF and AF were very similar. Trace differential components, including 9 flavonoids, 2 coumarins, 5 limonoids, and 26 volatile compounds, were screened as potential chemical markers to distinguish between QAF and AF. Additionally, the antioxidant capacity of QAF was found to be greater than that of AF. This research provides insights into the quality control and clinical application of QAF.