Excessive reactive oxygen species (ROS) can oxidatively damage DNA to cause severe biological consequences. In the study, a natural flavonoid, myricitrin (myricetin‐3‐O‐α‐L‐rhamnopyranoside), was found to have a protective effect against hydroxyl‐induced DNA damage (IC50 159.86 ± 54.24 μg/mL). To investigate the mechanism, it was determined by various antioxidant assays. The results revealed that myricitrin could effectively scavenge ·OH, ·O2−, DPPH· (1,1‐diphenyl‐2‐picrylhydrazyl radical), and ABTS+· (2,2′‐Azino‐bis(3‐ethylbenzothiazoline‐6‐sulfonic acid) radicals (IC50 values were respectively 69.71 ± 5.93, 69.71 ± 5.93, 25.34 ± 2.14, and 1.71 ± 0.09 μg/mL), and bind Cu2+ (IC50 27.33 ± 2.36 μg/mL). Based on the mechanistic analysis, it can be concluded that: (i) myricitrin can effectively protect against hydroxyl‐induced DNA oxidative damage via ROS scavenging and deoxynucleotide radicals repairing approaches. Both approaches can be attributed to its antioxidant. From a structure‐activity relationship viewpoint, its antioxidant ability can be attributed to the ortho‐dihydroxyl moiety, and ultimately to the stability of its oxidized form ortho‐benzoquinone; (ii) its ROS scavenging is mediated via metal‐chelating, and direct radical‐scavenging which is through donating hydrogen (H·) and electron (e); and (iii) its protective effect against DNA oxidative damage may be primarily responsible for the pharmacological effects, and offers promise as a new therapeutic reagent for diseases from DNA oxidative damage.