The invention discloses a microorganism-enhanced selenium-enriched vegetable hydroponic method and application thereof, which comprises the steps of vegetable seedling cultivation, vegetable seedling hardening, microbial root system colonization, vegetable transplantation and the like. The method of the present invention colonizes Escherichia coli EG16 in the root of vegetables, compared with the general hydroponic method, it can effectively promote the growth of vegetables, reduce the physiological stress of Se, improve the stress resistance of vegetables, and increase the yield of vegetables; and the method of the present invention The concentration range of medium selenium is suitable, it will not cause poisonous damage to plants, and the production waste liquid is not easy to cause environmental pollution. In the process of hydroponics, only the nutrient solution containing selenium needs to be replenished in time, the daily management process is less, the operation is simple, and the overall operating cost is low.