The purpose of this study is to treat the ballast water by shear stress without an environmental pollution and to find out the optimal treatment conditions. The ballast water problem is issued up as the trade activated and the cargos mobilized. To improve this problem, International Marine Organization(IMO) make the rule about the ballast water treatment with specific restrictions. Although many countries have been studying about the ballast water treatment technology, there is almost no technology that can treat the microorganisms under 50μm withoutany secondary pollution. In this study, we tried to treat ballast water by applying shear stress as the physical treatment for the sterilization and tried to find out the optimal conditions including the 100% sterilizing rate and the best economic condition.