The invention discloses a seed sterilization method during aseptic seeding of orchids. The method comprises a sterilization method for non-cracked fruit pods and a seed sterilization method for cracked fruit pods. The method specifically comprises the following steps: removing persitent perianth, gynandrium and carpopodium of the fruit pods when the pods are not cracked, cleaning with running water, disinfecting in a 5% sodium hypochlorite solution for 20 minutes, disinfecting the surface with 75% alcohol for 3 minutes, and directly firing on an alcohol lamp to remove alcohol on the surface of the pods so as to complete disinfection; and placing the seeds in a 300-mesh nylon mesh bag with the size of 3cm*4cm when the fruit pods are cracked, performing hot melting and sealing, placing the nylon mesh bag in a 10.0ml of centrifuge tube, adding a disinfectant into the centrifuge tube so as to enable the liquid level of the disinfectant to immerse the nylon mesh, standing for 20-40 minutes, and flushing with sterile water for several times until disinfection is completed. The disinfection time can be effectively controlled, the surface disinfection effect is guaranteed, the operation is simple and convenient, the seed vigor is not influenced, and the method is a disinfection method suitable for orchid seeds and similar tiny seeds.