In order to tackle the ecological destruction and environmental pollution problem in port caused by the discharge of the untreated ship exhaust and ballast water, an integrated treatment system of exhaust and ballast water in ship was developed. The system includes three modules, that is, electrochemical seawater modification reactor, ballast water treatment reactor and exhaust purification scrubber. Seawater is treated in the seawater modification reactor by membrane separation and electrochemical technique, while a strong oxidizing stream and an alkaline stream are formed. The strong oxidizing stream is used in the deactivation of microorganisms in the ballast water and to oxidize NO and SO2 to less hazardous and more soluble SO3 and NO2. The alkaline stream, in other hand, neutralizes and absorbs the acidic gas in the exhaust. This system can effectively treat both the exhaust and ballast water problem in ship with much reduced treatment volume. Thus, it is highly applicable for the treatment in ship.