The invention provides a polygonatum cyrtonema immature embryo culture micro-stem tuber breeding method. The method comprises the following steps: selection of excellent single plant of polygonatum cyrtonema, stripping of immature seed immature embryos, induction culture of immature embryos, induction formation of micro stem tuber, propagation of micro stem tuber, and direct transplanting of micro stem tuber for seedling establishment. The polygonatum cyrtonema immature embryo culture has the advantages of rapid growth, strong differentiation force, and large propagation coefficient, and propagation and transplanting of the micro stem tuber have the advantages of fast propagation speed, large quantity, short period, convenient transplanting, storage resistance, transport resistance, direct transplanting, simple management and high survival rate; so that the seedling growing problems of slow breeding and seeding formation of the polygonatum cyrtonema seeds, low rhizome propagation coefficient and high cost in the prior art can be solved, polygonatum cyrtonema seedling can be rapidly breed, and the method is suitable for industrial large-scale production.