The invention relates to a method for preparing indirubin with simple and convenient operation, small pollution and little equipment investment. The method comprises the following technological steps:adding methanol with the quantity of 5-10 times of raw materials into the raw materials, extracting by ultrasonic for 1-3 times, extracting for 0.2-1 hour each time, merging extracting liquid, recovering the methanol by depressurization, concentrating, filtering liquor by a macroporous resin column, eluting with water firstly, removing impurities, then eluting with ethyl acetate, concentrating eluent, adopting chromatographic separation by an alumina column, eluting with chloroform-ethyl acetate, concentrating eluent, recrystallizing with methanol-acetone, washing, drying to obtain the indirubin. By adopting the invention to prepare the indirubin, the product purity is high and industrialization amplification is easy to realize.