A code developed using the flux-difference splitting scheme on the hybrid Cartesian/immersed boundary method is applied to simulate three-dimensional internal waves. The material interface is regarded as a moving contact discontinuity and is captured on the basis of mass conservation without any additional treatment across the interface. Inviscid fluxes are estimated using the flux-difference splitting scheme for incompressible fluids of different density. The hybrid Cartesian/immersed boundary method is used to enforce the boundary condition for a moving three-dimensional body. Immersed boundary nodes are identified within an instantaneous fluid domain on the basis of edges crossing a boundary. The dependent variables are reconstructed at the immersed boundary nodes along local normal lines to provide the boundary condition for a discretized flow problem. The internal waves are simulated, which are generated by an pitching ellipsoid near an material interface. The effects of density ratio and location of the ellipsoid on internal waves are compared.