Disclosed herein are an apparatus and method for treating ship ballast water, wherein electron beams are irradiated into the ballast water to induce radiolysis of the water, and harmful marine organisms present in the ballast water are killed by radicals produced by the radiolysis. The electron beams are continuously irradiated into the ballast water under operating conditions of an energy of 0.5-5 MeV, an electron beam irradiation dose of 0.1-30 kGy and a flow rate of 1-200 m3/hr.