Flavonoids have important biological activities, such as anti-inflammatory, antibacterial, antioxidant and whitening, which is a potential functional food raw material. However, the biological activity of Fengdan peony flavonoid is not particularly clear. Therefore, in this study, the peony flavonoid was extracted from Fengdan peony seed meal, and the antioxidant, antibacterial and whitening activities of the peony flavonoid were explored. The optimal extraction conditions were methanol concentration of 90%, solid-to-liquid ratio of 1:35 g:mL, temperature of 55 °C and time of 80 min; under these conditions, the yield of Fengdan peony flavonoid could reach 1.205 ± 0.019% (the ratio of the dry mass of rutin to the dry mass of peony seed meal). The clearance of Fengdan peony total flavonoids to 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical, hydroxyl radical and 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radical could reach 75%, 70% and 97%, respectively. Fengdan peony flavonoid could inhibit the growth of the Gram-positive bacteria. The minimal inhibitory concentrations (MICs) of Fengdan peony flavonoid on S. aureus, B. anthracis, B. subtilis and C. perfringens were 0.0293 mg/mL, 0.1172 mg/mL, 0.2344 mg/mL and 7.500 mg/mL, respectively. The inhibition rate of Fengdan peony flavonoid on tyrosinase was 8.53–81.08%. This study intensely illustrated that the antioxidant, whitening and antibacterial activity of Fengdan peony total flavonoids were significant. Fengdan peony total flavonoids have a great possibility of being used as functional food materials.