Abstract: The microwave and aqueous two-phase system co-extraction of total flavonoids from fructus gardeniae and the anti-oxidation activity of extract was studied. The optimum extracting conditions were confirmed through the single factor experiments and orthogonal experiments. The extract's scavenging effects on O ^2-· and · OH were evaluated by using methods of pyrogallol autoxidaion and phenanthroline with VC and rutin as reference substance. The best conditions for distillation were as follows: 3 min of continuous microwave radiation, 1:30 solid-liquid ratio, 350W of the microwave power, 4 g of the K₂HPO₄, and 80% of the ethanol concentration; and the yield of the flavonoid could reach 1.71% at the optimum conditions. Flavonoids has limited scavenging effect onO^2-· and ·OH, but its scavenging effect onO^2-· was weaker in contrast with V_C the scavenging effect on ·OH was weaker than Vc and rutin. And the clearance rate increases with the amount of flavonoids.