Nine flavonoids were isolated and characterized from the leaves of Zanthoxylum bungeanum. Their structures were elucidated by spectroscopic techniques as quercetin (1), afzelin (2), quercitrin (3), trifolin (4), quercetin-3-O-β-D-glucoside (5), isorhamnetin 3-O-α-L-rhamnoside (6), hyperoside (7), vitexin (8) and rutin (9). All compounds were isolated from the leaves of Z. bungeanum for the first time. Five compounds (2, 4, 5, 6 and 8) were found for the first time in the genus Zanthoxylum. To learn the mechanisms underlying its health benefits, in vitro (DPPH, ABTS, FRAP and lipid peroxidation inhibition assays) and in vivo (protective effect on Escherichia coli under peroxide stress) antioxidant activities of the nine flavonoids were measured. Quercetin and quercetin glycosides (compounds 1, 3, 5, 7, 9) showed the highest antioxidant activity. Structure-activity relationships indicated that the -OH in 4' position on the B ring and the -OH in 7 position on the A ring possessed high antioxidant activity; B ring and/or A ring with adjacent -OH groups could greatly increase their antioxidant ability. Also, due to the different structures of various flavonoids, they will certainly exhibit different antioxidant capacity when the reactions occur in solution or in oil-in-water emulsion. These findings suggest that Z. bungeanum leaves may have health benefits when consumed. It could become a useful supplement for pharmaceutical products and functional food ingredients in both nutraceutical and food industries as a potential source of natural antioxidants.