The invention discloses a technology for restoring a heavy-metal polluted seedling-throwing planting rice field by using a root system micro geochemical barrier technology. The method comprises the following steps: (1) mixing rice field seedling raising soil with a heavy-metal repairing material, carrying out rest seedling growing processes according to a local cultivation system; and (2) adding the heavy-metal repairing material into farmland in processes of base fertilizer application and later-period topdressing, and carrying out cultivation in other farming processes according to local habits. In the technology, according to the characteristic that a root system absorbs substances in soil in a growth process of rice, a proper mineral material is selected to form chemical barriers on the periphery, so that the absorption effect of the root system is protected, and absorption of the root system to the pollutants is reduced or blocked. When the method is used to repair and treat a rice field polluted by cadmium and lead, the effective state of cadmium in the farmland can be reduced by 40%, and the repaired rice can reach a standard.