In the stratified closed water systems such as bays, lakes, and river mouths flowing into sea, the unique phenomena caused by the density differences are observed. Numerical simulation is useful for investigating such phenomena and three-dimentional numerical models are required when it have occured under the effects of changeable wind direction and complicated ground shape. In this paper, a three-dimensional numerical model which employs LES and CIP methods is proposed for the purpose of calculating incompressible density current. The model is closs-checked by the results of an experimental density flow in a flume, in which the movement of density front and internal seiche can be observed. The applicability of such a process is confirmed by the calculated results of miglation of density front, vortexes behind it, diffusion of inner density boundary, and period of internal seiche.