The invention relates to a method for preparing genistein and daidzein by using red clover isoflavone, which belongs to the field of chemical synthesis technique. Red clover isoflavone formononetin and biochanin-a extract are served as raw materials and subjected to one-step chemical modification: the red clover isoflavone formononetin is converted into the daidzein, and the red clover isoflavonebiochanin-a is converted into the genistein simultaneously and respectively; then, the products of the daidzein and the genistein are prepared after extraction, purification and separation are carried out. The preparation method of the invention has the advantages of simple and easy operation, over 96 percent of conversion rate and using the red clover which is renewable biological resource as raw materials, without occupying food resources and quality land; the red clover has high isoflavone content, thereby reducing the production cost for preparing the genistein and the daidzein.