The invention provides blue-green algae deep-well algae killing equipment and a blue-green algae treatment method thereof. The equipment comprises an inner barrel and an outer barrel, which are arranged in a shore base and are mutually nested to form a water passing gap, and a water guide pipe and a water returning pipe which stretch toward a water body from the shore base and are provided with water inlets; the water guide pipe extends through the outer barrel and is communicated with the inner barrel; the water returning pipe is communicated with the outer barrel, and a water discharging device, which is higher than the bottom of the water body, is assembled at the tail end, located in the water body, of the water returning pipe. According to the blue-green algae deep-well algae killing equipment and the blue-green algae treatment method thereof, provided by the invention, the inner barrel and the outer barrel, which are used for forming hydrostatic pressure at the bottom and carrying out crushing treatment on blue-green alga, can be arranged on the shore base, and blue-green algae fragments formed by crushing of the hydrostatic pressure are directly discharged into the water body through the water returning pipe, so that efficient biological treatment on the blue-green alga is realized; the bursting of the blue-green alga is effectively prevented, and the bursting of the blue-green alga is inhibited from a source; the prevention and treatment cost of the blue-green alga is reduced, and odor is prevented; the blue-green algae deep-well algae killing equipment has the advantages of small difficulty of installation and maintenance.