This study is aimed at determining the relationship of flavonoid structures to their chemical and intracellular antioxidant activities. The antioxidant activities of 60 flavonoids were investigated by three different antioxidant assays, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, oxygen radical absorption capacity (ORAC), and cellular antioxidant activity (CAA) assays. The result showed 6 flavonoids as good cellular antioxidants evaluated for the first time. The cellular antioxidant activities of compounds 7-methoxy-quercetin, 3-O-methylquercetin, 8-hydroxy-kaempferol, quercetin-3-O-α-arabinofuranose, kaempferol-7-O-glucopyranoside, and luteolin6-C-glucoside were linked with the upregulation of antioxidant enzyme activities (superoxide dismutase, catalase, and glutathione peroxidase). A structure-activity relationship suggested that 2,3-double bond, 4-keto groups, 3′,4′-catechol structure, and 3-hydroxyl in the flavonoid skeleton played important roles in the antioxidant behavior. Furthermore, the cell proliferative assay revealed a low cytotoxicity for 3-O-methylquercetin. The present results provide valuable information for the dietary application of flavonoids with different structures for high antioxidant.