The present invention relates to a method of driving a ballast water treatment system. The ballast water treatment system includes an air compressor for compressing air, an air receiver tank for storing the compressed air, an oxygen generator for generating oxygen from the air, an oxygen receiver tank for storing the oxygen, an ozone generator for generating ozone from the oxygen, a ballast water pump for pumping ballast water, an inflow line for transferring the ballast water, an ozone injector for injecting the ozone into the inflow line, and a destructor for purging the ozone. The driving method includes a step of pressing a stop button to stop the ballast water treatment system, a step of purging ozone generated in the ozone generator, and a step of stopping each device of the ballast water treatment system.