The invention provides a molecular breeding method for quickly obtaining a large number of new transgenic Saussurea involucrata varieties. The method comprises the following steps of: transforming expression vectors carrying target genes into agrobacterium rhizogenes; co-culturing the agrobacterium rhizogenes and Saussurea involucrata explants which are cultured by plant tissue culture technologyto ensure that the target genes are inserted into genomes of the explants; after resistance screening, detecting resistant calli or resistant buds by a molecular detection method to obtain resistant plants containing the target genes, namely the transformed plants, wherein a large number of transformed plants can be obtained by a bud multiplication method; and planting the transformed plants to obtain a large number of new transgenic Saussurea involucrata varieties. A large number of new transgenic Saussurea involucrata varieties can be obtained in five months, so the urgent requirements of culturing, screening and doing biological and pharmic academic research on Saussurea involucrata superior lines are met, precious genetic materials for germplasm resource innovation of the Saussurea involucrate are provided, and the method has obvious ecological, economic and social benefits on the sustainable development of the Saussurea involucrata.