The invention discloses a fuel oil filling automatic control system for a marine refueling ship and a control method. The fuel oil filling automatic control system comprises a wave height meter, a PIDcontroller, a comparison circuit, an automatic control valve and an oil conveying hose. The comparison circuit and the automatic control valve are both electrically connected with the PID controller,the wave height meter is electrically connected with the comparison circuit, and the automatic control valve is connected with the oil conveying hose. The fuel oil filling automatic control system has the characteristic of being capable of improving the oil conveying efficiency and safety.