The invention relates to an ultrasonic sea chest cavitation sterilization machine and an ultrasonic ballast water cavitation sterilization machine for a ship sea chest, a method for killing and inhibiting marine organisms by ballast water, and a system device, which are researched and developed for cross-sea propagation of harmful microorganisms, funguses and pathogens caused by injecting and discharging the harmful microorganisms, the funguses and the pathogens in the water at different places along with a ship, and cross contamination of a sea area caused by non-control discharge of the ballast water when the goods are loaded and unloaded and the seawater (or fresh water) are injected and discharged in running, anchoring and mooring processes of the ship; the intrusion of the foreign species can cause hazard to marine ecology, and the hazard is listed as one of four marine hazards by International Environment Fund (CEF). According to the invention, ultrasonic wave is made to a device to be connected to an inlet of the ship sea chest and a pipeline of the ballast water in series, and ultrasonic cavitation cell crushing can be carried out on the harmful microorganisms, the funguses and the pathogens in the seawater (or fresh water) by utilizing a function of ultrasonic wave for crushing the cells, so that the inactivating and sterilizing treatment effects can be realized, and the method can play the following roles that: 1, cavitation sterilization is carried out on the water entering into the sea chest through the ultrasonic sea chest cavitation sterilization machine, so that the cells are crushed, algae and shellfish microorganisms in a coarse filter of the sea chest are killed, and the possibility of blockage of the coarse filter of the sea chest and a water inlet pipeline can be reduced, thus the algae and shellfish microorganisms cannot produced and survived in a ballast water pipeline, a water discharge pipeline, a water pump and a filter and the pipeline is kept unblocked; and 2, ballast and discharge pipelines are internally connected with the ultrasonic ballast water cavitation sterilization machine in series, ultrasonic cavitation is carried out on the seawater (fresh water) entering into a ballast tank, so that the cells are crushed, and the residual algae and shellfish microorganism pathogens are inactivated and killed, thus the bacterium in the seawater (fresh water) into the ballast tank reach requirements of international maritime organization (IMO) International Ship Ballast Water and Sediment Control and Management Convention (latter called convention), and one of four marine hazards, that is to say, the intrusion problem of the foreign specifies, can be solved and eliminated. The invention provides guarantee of technical equipment for equipping ballast water equipments of all ocean going vessels before 2017 according to the requirement of the international maritime organization (IMO) convection.