Abstract: In current domestic situation, the by-products containing with flavonoids such as epimedin A, B, C was not being used during the icarrin production from epimedium extract. In this paper, the enzyme from A.sp.y 39 strain was filtered for transformating epimedin A, B, C in waste offscum of epimedium extract. The 150 g of the market epimedium extract was dissolved in 60% ethyl alcohol for decoloring by D-280 macroporous resin, and then 30.5 g of icariin was obtained from above discolored epimedium extract by crystallization method.Then, 16.6 g of icariin was obtained from the waste offscum containing epimedin A, B and C by the enzyme from A.sp.y39 strain.Finally, 47.1 g of icariin ( the purity was over 90%) was obtained from 150 g of epimedium extract by above enzyme transformation methods, the yield of icariin was rised from 20.3% to 31.4%.Compared with the traditional method, the extraction rate of icariin was increased by more than 50%, which provided the basis for saving epimedium resources.