The utility model relates to a shipborne micro-filtration algae removal system. A hull body comprises a bow and a stern; the bottom of the bow is provided with a water inlet which is provided with a grille mesh; a water taking chamber is arranged in the bow; the middle of the water taking chamber is provided with an inflow gate which divides the water taking chamber into a front chamber and a rear chamber; the end of the rear chamber is provided with a lift pump; the lift pump guides raw water into a drum through a water delivery pipe ; a micro-filtration main unit comprises a filter box and a water reservoir; the raw water filtered flows out of an overflow hole and flows into the water reservoir; the output end of the water reservoir is provided with a water outlet whereby the raw water filtered is discharged. The shipborne micro-filtration algae removal system is reasonable in design, compact in structure, simple to manufacture, high in flow, low in operation and maintenance costs and long in service life; sold matter filtered is all removed from the drum continuously, filtering is through, filter cloth is never pressurized, the service life of the system is long, the different hull bodies can be designed according to conditions of different waters, the micro-filtration main units different in amount and type can be mounted to adapt to the different waters, and the system can be widely applied.