The paper studied the extracting of flavonoids in the nutlets of Clausena anisum-olens with Microwave assisted extraction (MAE). The single factor and orthogonal designmethods L9(34) were applied for the optimal technologicalconditions：70 ◦C，(EtOH)=60 %，m(the nutlets of Clausena anisum-olens):m(EtOH)=1:16，440 W，10 min. Under the optimized conditions, the extraction percent of total flavonoids is about 1.340 % from the nutlets of Clausena anisum-olens.There was a positive correlation between hydroxyl radical scavenging activity and concentration of total flavonoids from the nutlets of Clausena anisum-olens.Observed at five experimental levels, and the hydroxyl radical scavenging rates at the concentration level of 0.442 g/L were 81.4 %.