Flavonoids were extracted from buckwheat powder by the microwave-assisted ethanol-ammonium sulfate aqueous two-phase system. The optimal extraction system of flavonoids from tartary buckwheat powder was determined through single factor experiments and the optimal concentration of ethanol and ammonium sulfate dosage were obtained. The results showed that the method of microwave assisted aqueous two-phase extraction was suitable for flavonoids extraction from tartary buckwheat powder. The extraction conditions were optimized by the response surface method and the optimized conditions were 30% ethanol as extraction agent, the microwave power 550W, extraction time 70s, and the material-to-liquid ratio 0.02g/mL. The yield of flavonoids was 1.38% under the optimized conditions.