The invention relates to a method for effectively converting Geniposide into Genipin by stimulating the conversion of microbes in the in vivo intestinal tract through an in vitro microbial fermentation process. The method is characterized in that: a traditional Chinese medicine cape jasmine is fermented by the high yield strain of beta-glucosidase screened and preserved in a laboratory of the inventors, and an optimum condition for obtaining the product Genipin through the microbial conversion is obtained by optimizing through single factor experiments. According to the method of the invention, Geniposide in Genipin in hydrolyzed under mild conditions, so a defect of the effective component loss of traditional methods is avoided; and the scale conversion of the effective component Geniposide of cape jasmine is realized under in vitro controllable conditions with a modern microbial fermentation engineering technology, so the method of the invention has large economic benefits and social benefits, and has a wide market exploitation prospect.