The invention discloses a method for realizing rapid separation and resource utilization of cyanobacteria in water. Water containing rich cyanobacteria is sent to a water storage tank, cyanobacteria in water is intercepted and filtered by means of an external membrane separation device, the membrane separation device adopts a cross-flow filtration manner, and the flow speed in a membranous tube is controlled to range from 0.1 m/s to 5 m/s; filtered water is sent to a clean water tank, and a concentrated cyanobacteria solution circulates to reach the water storage tank; the concentration of cyanobacteria in the water storage tank can reach 10-50 g/L (the content of chlorophyll alpha) through cyclic separation of cyanobacteria and water; the concentrated cyanobacteria solution in the water storage tank is sent to an anaerobic tank for anaerobic digestion treatment, and generated biogas is recycled; the water storage tank can also be used as an anaerobic digestion tank. The method is suitable for treating surface water containing cyanobacteria in medium or low concentration and has the advantages of good cyanobacteria separation effect, high flexibility, high resource utilization rate and low operation cost.