The invention provides a device for treating neuston pollution by microwave. The device comprises a microwave treatment module, a lift adjustor and a buoy. The device is characterized in that the device is impelled on the water by drive of dynamic equipment; stream with the neuston flows into a treatment cavity of the microwave treatment module from a water inlet of the microwave treatment module, after receiving microwave radiation, living cells of the neuston are killed, and the living cells flows out of a water outlet; the lift adjustor is used for adjusting the draft of the microwave treatment module, namely the thickness of a water layer to be treated; the buoy makes the whole device for treating the neuston pollution by the microwave float on the water; and a power supply required by the device can be supplied by a generator, a storage cell, solar energy and wind energy. The device kills the neuston by a physical method, does not have residue or pollution, and does not cause public hazard, not only can be used for killing blue algae, water lettuce and other floating plants, but also can be used for killing wiggler and other harmful plankton.