Internal waves in a bay have an effect on vertical mixing and mass transfer. Toestimate sources and roles of the internal waves, we have to carry out computation with high resolution by using a three-dimensional non-hydrostatic model. As it is hard to carry out it now, a multi-layer model is considered to be one of the most suitable model. However, internal hydrolic jumps occur frequently on an interface between layers because of small density difference and great velocity (Internal Froude number>1.0). In previous studies, a flow field including both rapid and streaming flow has been solved by CIP-m scheme in which a finite difference method is used. But it is better to use a finite difference method (FEM) because the shape of a bay are complicated and FEM can be applied to any shape. In this study our purpose is to develop CIP-m FEM. The result of an experiment was consistent with that of computation.