Artemisiae Argyi Folium (Aiye in Chinese) has been widely used since ancient times. In the Lingnan region (Southern China), the leaf of Artemisia verlotorum Lamotte, which is named Hongjiaoai (HJA) because the roots are red (Hongjiao means red foot in Chinese), has been used as a local substitute for Artemisiae Argyi Folium. The plant has a long medicinal and edible history that can be traced to the Jin Dynasty. However, there is no systematic and reliable method to control the quality of Artemisiae Verlotori Folium. In this study, a comprehensive method involving high-performance liquid chromatography coupled with diode array detection and quadrupole-time-of-flight high-definition mass spectrometry was established to identify and quantify eight constituents (including organic acids and flavonoids) in Artemisiae Verlotori Folium and Artemisiae Argyi Folium as well as high-performance liquid chromatography fingerprints of the two varieties. Moreover, dissimilarities of chemical compositions among the two varieties were further investigated by orthogonal partial least squares discrimination analysis and cluster analysis. This research not only explored the similarities and differences between Artemisiae Verlotori Folium and Artemisiae Argyi Folium in eight components but also provided a qualitative and quantitative analytical method that quickly, accurately, and comprehensively assesses the quality of Artemisiae Verlotori Folium.Article Related Abbreviations: DAD, diode array detector; HCA, hierarchical clustering; HPLC-DAD-Q-TOF-MS, HPLC coupled with diode array detector and quadrupole-time-of-flight mass spectrometry; OPLS-DA, orthogonal partial least squares discriminant analysis; TCM, traditional Chinese medicine; VIP, variable importance in the projection.