Abstract: Combined with analytic hierarchy process-entropy weight method, the effects of microwave power, liquid-solid ratio, extraction time, extractions times and particle size were investigated in single factor test using the yield of baicalin, wogonoside, baicalein, wogonin and paste yield as the indexes. Taking the comprehensive score as the response value, the microwave extraction process of Scutellaria baicalensis was optimized by the Box-Behnken response surface test at four factors and three levels. The micro-morphological changes of medicinal powder before and after extraction were observed by SEM. The results showed that the optimal extraction process conditions obtained by BBD response surface method were microwave power of 390 W, liquid-solid ratio of 56 mL/g, extraction time of 472 s, and particle size of 80 mesh (180 μm). At this time, the yield of baicalin, wogonoside, baicalein and wogonin were 16.82%, 3.46%, 0.30% and 0.31%, respectively, the paste yield was 73.73%, and the comprehensive score was 10.75. The extraction effect of this process is better than that of common reflux extraction, and the subjectivity and objectivity of the evaluation results are realized.