Abstract: This invention involves ship flue gas desulphurization method and system. It employs seawater to reduce SO2 and other pollutant discharged by ship. The method includes seawater scrub, acidic seawater transfer, deacidification, and discharge processes. The system includes a scrubber and a water-saving deacidification device. Upper portion of the scrubber comprises a scrubbing section which is connected with scrubbing seawater pump by pipelines. Lower portion of the scrubber comprises a cooling section. One end of the scrubber links the ship engine smoke pipe by a scrubbing inlet pipe, and the other end links the scrubber to a scrubbing outlet pipe. The water-saving deacidification device lies below the scrubber and is connected with it. The water-saving deacidification device is coupled to a blending seawater pump, fan, and total drain pipe for discharging seawater after deacidification. This invention provides high desulphurization efficiency, and requires small seawater quantity.