The invention discloses a method for cultivating rhizoma polygonati seedlings in greenhouses. The method includes steps of 1), picking ripe rhizoma polygonati fruits; 2), drying the ripe rhizoma polygonati fruits; 3), disinfecting humus soil; 4), preparing mixed media; 5), preparing nutrient media; 6), carrying out cultivating and reproducing by the aid of nutrition cups; 7), planting the rhizoma polygonati fruits in the greenhouses at the internal temperatures of 22-25 DEG C under the control, keeping the greenhouses ventilated, illuminating the rhizoma polygonati fruits for the illumination time of 10-15 hours/day, regularly spraying disinfectant liquid, regularly spraying clear water after the rhizoma polygonati seedlings emerge and illuminating the rhizoma polygonati seedlings for the prolonged illumination time of 15-20 hours/day; 8), only reserving a strong rhizoma polygonati seedling in each nutrition cup when the rhizoma polygonati seedling grows and the height of the rhizoma polygonati seedling reaches 2.5-3.5 cm, and irrigating the roots of the rhizoma polygonati seedlings with potassium fertilizer water with the proportion of 80-150 times before the rhizoma polygonati seedlings are transplanted; 9), transplanting the rhizoma polygonati seedlings. The method for cultivating the rhizoma polygonati seedlings in the greenhouses has the advantages of high reproduction sprouting rate, high survival rate after emergency of the seedlings, few seedlings without rhizomes after emergency of the seedlings, few plant diseases and insect pests, high growth weights of rhizomes of individual plants, short growth cycle and convenience in transportation.