The invention provides a method for controlling an eutrophic water body by selecting a grass type lake native aquatic plant. In the method, superior aquatic plant species in a current season in a target lake are selected and previously cultured, and the following steps are executed: 1, filling the substrate sludge and lake water of the target lake into a container in a semi-closed greenhouse to construct an aquatic plant and natural alga co-culture system; 2, adding a nutrient solution to the co-culture system, then selecting uniformly grown plants from each species of previously cultured aquatic plants, and respectively planting into the co-culture system to ensure that each specie of aquatic plants constructs an aquatic plant community; 3, sampling and detecting the co-culture system with the aquatic plant communities planted according to a preset time interval, and selecting proper native aquatic plants used for controlling the eutrophic water body according to a detection result and a predetermined target.