The invention provides a system and a method for cyclone flotation treatment of algae-containing wastewater. The system comprises a mixer, a filter and a tank body integrally placed in a vertical manner, wherein the position of the inner cavity close to the bottom part of the tank body is horizontally provided with a hollowed-out plate; an inner drum with the top part opened and the bottom part closed is vertically arranged on the hollow-out plate; the area of the interior of the inner drum forms a cyclone flotation zone; the area between the inner drum and the inner wall of the tank body form a precipitation zone; the interior of the cyclone flotation zone, from bottom to top, is successively provided with a bubble generator and swirl vanes capable of enabling water to generate cyclone through horizontal rotating; the water inlet of the tank body communicates with a water inlet channel which is downward arranged and extends to the upper part of the swirl vanes; and the top part of the tank body is provided with a scum concentration zone and an effluent weir used for effluent overflowing of clear water. The method provided by the invention comprises the following steps: adding a flocculant and carrying out a flocculation reaction, and subjecting the filtered wastewater to cyclone flotation so as to remove impurities with a density larger than or less than the density of water, wherein the removal efficiency to algae is high.