A method for producing germinating fungus production strains for sexual propagation of Gastrodia elata by using cottonseed hulls as a main material comprises the following steps: 1) material preparing: the cottonseed hulls, corn meal, rice bran, gypsum and sucrose are taken in parts by weight; 2) material mixing: the components are mixed and stirred uniformly, then water is added until the water content of a compost reaches 60%-80%, and the compost is uniformly mixed; 3) bagging: the uniformly stirred compost is accommodated in polyethylene or polypropylene material bags; 4) sterilizing: the material bags are subjected to high-pressure sterilization at the temperature of 121 DEG C and the pressure of 101 kPa; 5) inoculating: germinating fungus strains are dug from a stock seed bottle and transferred into the material bags; 6) culturing: the material bags after inoculating are transferred to a light-shielding culturing chamber and cultured at the temperature of 25 DEG C until germinating fungus mycelia grow fully in the material bags. The time for a germinating fungus to grow fully in the bags is shortened, the Gastrodia elata seed germination rate is increased, and the decay resistance of a culture medium is enhanced. The produced germinating fungus strains have the advantages of high yield, uniform growth and unified growth period and is applicable to sexual propagation of the Gastrodia elata.