The invention provides a method for strengthening shape transformation of endogenous phosphorus in substrate sludge of an enclosed type water body. The method comprises the following steps of adding limnodrilus hoffmeistteri to the substrate sludge of the enclosed type water body to be repaired; after the limnodrilus hoffmeistteri gets into the substrate sludge of the water body, performing aeration on overlying water for 1h, enabling the concentration of dissolved oxygen in the overlying water to be maintained to 2-4mg/L, enabling the aeration to be stopped for 5h, then performing aeration by using the operations of performing aeration for 1h and enabling the aeration to be stopped for 5h as a cycle; when the total bioactivity of the substrate sludge of the water body reaches 0.5-0.7 [mu]mol/(h.g) <-1> or above through the aeration, performing aeration on the overlying water for 2h, enabling the concentration of the dissolved oxygen in the overlying water to be maintained to 3-5mg/L, enabling the aeration to be stopped for 10h, and then performing the aeration by using the operations of performing aeration for 2h and enabling the aeration to be stopped for 10h as a cycle; and performing the aeration for 20-30 days so that a process of strengthening the shape transformation of the endogenous phosphorus of the substrate sludge of the enclosed type water body is completed. According to the method disclosed by the invention, a method for effectively controlling the release of the endogenous phosphorus can be provided.