BackgroundPlants in the genusArtemisiaare rich in active ingredients and specialized metabolites. Many of these compounds, especially flavonoids, have potential medicinal and nutritional applications, and are of growing interest to scientists due to their wide range of pharmacological and biological activities.Artemisiacultivars are commonly used as raw materials for medicine, food, and moxibustion in China. However, most of the metabolites produced byArtemisiaspecies have not been identified, and few studies have addressed differences in active compounds between species and cultivars.ResultsWe here investigated twoArtemisiacultivars, ‘Nanyangshiyong’ (NYSY) and ‘Nanyangyaoyong’ (NYYY), which are commonly used in foods and moxibustion, respectively. NYSY and NYYY were confirmed to beArtemisia argyicultivars. Total flavonoids contents and antioxidant activities were higher in NYYY than in NYSY. A total of 882 metabolites were identified in the samples; most of the potentially medicinally active compounds, especially flavonoids (e.g., flavone, flavonol, isoflavone, and anthocyanin), were up-regulated in NYYY compared to NYSY. Furthermore, most of the genes related to flavonoids biosynthesis were up-regulated in NYYY. Correlation analysis was used to identify putative members of transcription factor families that may regulate genes encoding key flavonoids biosynthesis enzymes.ConclusionsWe found that the antioxidant activities and flavonoids contents significantly varied between twoArtemisiacultivars of the same species. We also uncovered metabolomic and transcriptomic evidence of the molecular phenomena underlying those differences in flavonoids contents between the twoArtemisiacultivars. This study provides a wealth of data for future utilization and improvements ofArtemisiacultivars, and highlights a need to study the specific metabolite profiles of plants that are used in foods and medicines.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-023-04295-8.