The invention provides an ultrasonic algae removing method used in a water intake of a water head site, relating to an ultrasonic algae removing system used for removing the blue-green algae in the water body of the water head site, being applicable to the treatment of environmental water body pollution caused by mass propogation of algae due to eutrophication, belonging to the technical field of environmental protection in which ultrasonic cavitation technology is utilized to safely and economically remove the blue-green algae in the water body of the water head site. The ultrasonic algae removing device used in the algae removing method comprises a water entry region (4), an ultrasonic emitter array (1), a settling pool (2) and a water getting region (3) which are arranged in sequence, wherein each part is separated by a water baffling wall (6); the ultrasonic emitter array (1) is arranged between the water outlet of the water entry region (4) and the water inlet of the settling pool (2) and processes the water flowing through the ultrasonic emitter array (1); the ultrasonic wave (12) which is radiated by the ultrasonic emitter array (1) has an effect on the blue-green algae floating in the water body, leading the floating ability to lose, and the blue-green algae are settled in the settling pool (2) to ensure that no algae exit in the water body of the water getting region (3) of the water plant, thus achieving the purpose of removing the blue-green algae.