The invention which belongs to the field of ship ballast water processing equipment especially relates to a method and an apparatus for processing ship ballast water through filtration, ultraviolet and ultrasound. The apparatus of the invention comprises a water pump, a pressure transducer, a flowmeter, a filter, a comprehensive processing unit of ultraviolet and ultrasound, a control system, an electromagnetic valve and a pipeline. Water enters the filter through the water pump, then enters the comprehensive processing unit of ultraviolet and ultrasound to be subjected to biological inactivation, and is finally discharged. The synergetic disinfection of the ultraviolet-ultrasound unit allows the disinfection effect to be good, ultrasonic waves destroy protective layers of microbes, the ultraviolet radiation destroys DNA and RNA of the microbes, and the ultrasonic waves have certain cleaning effects on ultraviolet lamps. The apparatus of the invention, which can effectively kill the microbes in the ship ballast water, has the advantages of low energy consumption, high reliability, simple operation and maintenance, realization of one-key operation through an automatic control unit, and flexible selection of an installation platform according to practical cases.