In order to improve the comprehensive extraction rate of atractylodes macrocephala, the comprehensive extraction of atractylodis macrocephalae rhizomastarted with direct distillation usingdistilled water as solvent to give aqueous extracts and volatile oil. The residue went through further alcohol extraction to give ethanol extracts. orthogonal test was conducted with flavone yield as inspection target to obtain optimal extraction condition, namely solid/solvent (water) ratio of 1:20 (mL/g), distillation time of 5 h, solid/solvent (ethanol) ratio of 1:20 (mL/g), and microwave treatment time of 4 min. Such conditions yield 0.44% of flavone, 30.42% of polysaccharide, and a total 35.21% yield from water and ethanol extraction. Further, the anti free radical experiment was carried out on the extract obtained by the optimal process. The results show that: a scavenging activity of 21.96% with OH free radical was observed at 50μg/mL ratio of aqueous extracts, and that of ethanol extracts of the same ratio was 18.89%.The optimal scavenging activity of 17.62% with DPPH free radical was observed at 40μg/mL ratio of aqueous extracts, with a scavenging activity of 12.85%at ethanol extracts of the same ratio.