The invention discloses a method for breeding industrial hemp in a greenhouse and belongs to the field of crop planting. Due to the breeding operation needs of hemp, increasing-generation reproduction is performed in the greenhouse, and crossbreeding is performed. Preparation of greenhouse breeding is performed after hemp seed harvesting for seeding in autumn. The invention aims to provide a method for breeding the industrial hemp in the greenhouse. The method disclosed by the invention comprises the steps of soil loosening before seeding, disinfecting and fertilizing, soil ridging, seeding of industrial hemp, performing field management on seedlings, performing management in a growth period of the industrial hemp, pollinating the industrial hemp and harvesting the industrial hemp seeds. According to the method disclosed by the invention, the defects in an isolation method in the prior art are overcome, the land space utilization ratio of greenhouse breeding is increased, different hybridized combinations are completed in the same place, the isolation effect is excellent, the isolated heterogonous plant rate is controlled to be 1-5%, the heterogonous plant hybrid rate is reduced by 10-14% due to mixing of varieties, and the labor intensity of scientific research personnel is reduced.