The demand of retrofitting flue gas desulfurization (FGD) system on the operating ships is increasing as the approach of the entry into force of IMO regulation that sets limits on SOX emissions from the ship exhausts in the world. It focuses on the key technology problems that should be considered in the retrofitting process for the large container ship equipped with the mixed desulfurization system, such as the design and selection of the desulfurization system, the arrangement of the equipment and tanks, and the design of the funnel. It can provide the beneficial technical exploration and accumulation for the installation of mixed FGD system on the large container ships and other ships.