The invention belongs to the technical field of ship fuel oil supply, and particularly relates to a ship fuel oil supply system with a filtering function. The ship fuel oil supply system comprises anoil storage tank, a slag discharging opening, a filling pipe and an output pipe, wherein the slag discharging opening is connected to the center of the lower surface of the oil storage tank; through the cooperation function of a suction pipe and a suction head, the suction head is made of plastic materials, the suction head can float on fuel oil, accordingly, the fuel oil can be sucked from the upper side, and impurities are reduced; through the arrangement of suction sieve holes in the suction head, the impurities can be filtered from the suction source, and the impurities are reduced from entering the suction pipe; through the arrangement of a filtering device, the impurities in the output process can be filtered, and gas in the output pipe can be exhausted through the cooperation function of an inverted U-shaped pipe and a gas outlet; and opening and closing of the gas outlet can be controlled through a control valve, accordingly, gas exhausting can be conducted in time, and the normal fuel oil output function cannot be influenced.