In the prior work, we studied a ballast water treatment apparatus, which is secondary pollution free by using physical treatment of shear stress. The principle of this apparatus is smashing various microorganisms by shear stress generated between stationary outer cylinder and revolving inner cylinder. Because of various magnitude of shear stress according to the inner cylinder surface type and revolution speed, an appropriate surface type and optimum revolution speed should be studied by consecutive experiment to determine the reference data for commercial apparatus. Through a comparative study of disk type and cylinder type of ballast water treatment apparatus, cylinder type is turned out to be superb to disk type. In this study, we studied to determine the superior collaboration of cylinder type, groove type and knurling type of inner cylinder to non patterned outer cylinder, and to optimize the revolution speed and flow rate according to the gap between inner cylinder and outer cylinder. As a result, we could get perfect sterilization effect at groove type under the conditions of 250 mL/min of flow rate at 8,000 rpm and 500 mL/min of flow rate at 10,000 rpm respectively.