The present invention provides a ballast water treatment system including a reaction tank in which raw water and ozone are imported and made to react each other for a predetermined period of time to kill microorganisms existing in raw water, an ozone decomposer in which water containing residual ozone discharged from the reaction tank is imported and the residual ozone is decomposed, and a circulation pump installed between the reaction tank and ozone decomposer, forming a circulation system which removes the residual ozone by means of circulating the water containing the residual ozone between the reaction tank and ozone decomposer. Accordingly, this system dispenses with a deaeration tank which would require a wide space for installation, small cost and is able to be applied to existing ships easily.