This paper introduced a new method of "ingredient difference phonetypical cloning" for functional gene clone of medicinal plants, which might solve the difficulties in isolating genes encoding enzymes for the biosynthesis of secondary metabolites by usual ways. Concepts, mechanisms and methods were systematically introduced and possibility was proved by experiments. The method showed the extra superiority of for the isolation of the genes belonged to unknown metabolic pathway and little information about its sequences. The method provides a new way to isolate functional gene cloning from Chinese herbs and a fundament for the further study on medicinal plant genetic engineering.