The present invention relates to a method for preparing a Sohporae Fructus extract containing isoflavone. More particularly, the present invention relates to a method for preparing a Sohporae Fructus extract containing isoflavone in high concentration, which is characterized by the steps of hydrothermal extraction, enzyme treatment and ethanol extraction of Sophorae Fructus. A Sophorae Fructus extract containing a high concentration of aglycon-type isoflavone having an excellent bio-absorbability can be prepared by the method of the present invention.