The invention discloses a method for preparing cartharein and isocartharein from naringenin. The method adopts the microbial transformation process comprising the following steps: culture of a microorganism, transformation of a substrate and collection and purification of the final product. The microorganism is a Aspergillus niger strain 3.4628 (CGMCC No.3.4628), and the substrate is naringenin. The transforming strain Aspergillus niger 3.4628 used in the invention is easily available and can be used repeatedly with low cost. The naringenin is rapidly transformed to produce cartharein and isocartharein within a short time period; and the transformation process causes less pollution and has a simple process, and the naringenin as the substrate can be recycled. The method makes preparation of the two substances (cartharein and isocartharein) in a large scale with low cost possible, and provides an important contribution to theoretical studies and wide applications of medicinal value of cartharein and isocartharein.