Flavonoids have been documented to have good antioxidant activities in vitro. In recent years, reports on the antioxidant activities of flavone C-glycosides, a subclass of flavonoids, have attracted great attention. Despite the wealth of information on this subject, the correlation between structure and function is not well understood. In this work, the relationship between the structure and the antioxidant activity of 12 flavone C-glycosides extracted from the aerial part of winter linseed (Linum usitatissimum L.) was studied to fill the current gaps. Orientin, isoorientin, vitexin, isovitexin, swertisin, swertiajaponin, carlinoside, schaftoside, lucenin-1, lucenin-2, vicenin-1, and vicenin-2 were purified by preparative HPLC and by the drowning-out crystallization method. Then, the control of the purity and the confirmation of the chemical structures were assessed by LC-MS and NMR analyses. The antioxidant activity was evaluated using ABTS, CUPRAC, FRAP, and iron chelating activity in vitro assays. Luteolin and its flavone C-glycoside derivatives exhibited higher antioxidant activity than apigenin and its flavone C-glycosides derivatives. This could be attributed to the ortho-dihydroxyl groups at C-3′ and C-4′ of the B ring in the flavonoid skeleton, which seemed to play an important role in antioxidant behavior. These results indicate that the antioxidant activity of these compounds, derived from apigenin and luteolin, can be closely related to their structural characteristics, including the position and nature of the sugars, the number of hydroxyl groups, and the presence of methyl group.