Ballast water of ten billion tons are transferred by the ship annually in the world. Because alien creatures are destroying aquatic ecosystems, ballast water treatment is needed. Physical methods of treatment using the filtration method is hydrocyclone. The advantage of hydrocyclone is to create a simple structure and a easy separation of good performance. A commercial CFD code CFX 11.0 is applied to analyze hydrocyclone. According to the shape changes of the hydrocyclone, separation performance was compared. The results show that when you reduce the height of hydrocyclone, hydrocyclone separation efficiency is lowered.