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Flavonoids are well known for their extensive health benefits. However, few studies compared the differences between flavonoid O-glycoside and C-glycoside. In this work, flavonoid O-glycoside (isoquercitrin), C-glycoside (orientin), and their aglycones (quercetin and luteolin) were chosen to compare their differences on antioxidant activities and metabolism during in vitro digestion and in vivo. In vitro digestion, the initial antioxidant activity of the two aglycones was very high; however, they both decreased more sharply than their glycosides in the intestinal phase. The glycosidic bond of flavonoid O-glycoside was broken in the gastric and intestinal stage, while the C-glycoside remained unchanged. In vivo, flavonoid O-glycoside in plasma was more elevated than C-glycoside on the antioxidant activity; however, flavonoid C-glycoside in urine was higher than O-glycoside. These results indicate that differences of flavonoid glycosides and their aglycones on antioxidant activity are closely related to their structural characteristics and metabolism in different samples. Aglycones possessed higher activity but unstable structures. On the contrary, the sugar substituents reduced the activity of flavonoids while improving their stability and helping to maintain antioxidant activities after digestion. Especially the C-glycoside was more stable because the stability of the C–C bond is higher than that of the C–O bond, which contributes to the difference between flavonoid O-glycoside and C-glycoside on the absorption and metabolism in vivo. This study provided a new perspective for comparing flavonoid O-glycoside, flavonoid C-glycoside, and their aglycones on their structure–activity relationship and metabolism.