A method for controlling the growth of blue algae in a basin relates to the field of the restoration and protection of the natural ecology on the earth's surface. An ecological water treatment system was constructed for the basin with microorganisms, plants, animals, fillers and the like as main elements by building a novel ecological slope protection at the land-lake ecozone along the banks of the basin and planting eucalyptus in the basin water and/or on the bank of the basin, thereby effectively realizing the efficient nitrogen and phosphorus removal from the basin, controlling the spread of blue algae and improving the environmental water quality.