The invention discloses a method for establishing a freshwater lake ecosystem, and belongs to the technical field of freshwater environmental pollution control. The method for establishing the freshwater lake ecosystem comprises the following steps of water quality improvement, water level maintenance, land-water interface treatment, bottom mud improvement, food network chain establishment, waterquality monitoring and the like, and an algae inhibitor throwing device is also arranged. Conditions for restoring the water ecosystem are established through combination of physics, chemistry and biology, and nitrogen and phosphorus pollutants in water are effectively degraded and absorbed by match of warm and cold plants, so that pollution load of a water body can be effectively reduced, the water body is purified, and the water ecosystem is stabilized. Aquatic plants and aquatic animals are thrown to construct a reasonable food network chain, and a plurality of aquatic plants and aquatic animals can exert a synergistic effect, so that the effect is more obvious compared with the effect of singly planting aquatic plants or singly throwing aquatic animals, transparency of the water body is improved, nutrient salts are reduced, and construction and restore of the water body ecosystem are facilitated.