An ocean model using "cut-cell method" has been developed to simulate the flow field around three-dimensional complicated topography via the modification of the MEC model, an ordinary Cartesian coordinate model. In the developed model, the finite volume method is employed for the accuracy of mass- and momentum-conservations. As an application, the developed model is applied for the analysis of the tidal flow of a bay connected with the ocean by a very narrow and oblique channel. Although results by the original MEC model strongly depend on the direction of the channel, the results by the developed model show good agreement with theoretical values. Then, the developed model is applied for the analysis of the flow around a tall seamount in steady background currents. Those results are discussed in comparison with the results by the original MEC model.