Abstract: Hemerocallis citrina Baroni (daylily) is a medicinal and edible food with flavonoids as its core active ingredient. Daylily showed significant differences in flavonoids across varieties, thereby impacting their health benefits. This study selected four daylily varieties in the Datong, namely Datong (DT), Mallian (ML), Mengzi (MZ), and Huaiyang (HY), for metabolomics to unravel their flavonoid composition. DT exhibited the highest total flavonoid content (TFC), while MZ demonstrated the strongest antioxidant potential. There were ten highly differential flavonoid metabolites in four daylily varieties that had a significant positive correlation with their antioxidant activity. Notably, the levels of these metabolites in MZ were the highest, corresponding to its strongest antioxidant activity. Network pharmacology analysis revealed that antioxidant targets associated with key flavonoids in daylily were primarily focused on PI3K-AKT signaling pathway, identifying AKT1 and EGFR as the core antioxidant targets. Molecular docking studies demonstrated their interaction mechanisms, suggesting that daylily flavonoids might attenuate the oxidative stress. This research provides critical insights for selecting and cultivating daylilies with enhanced health benefits.