Evolutions of internal waves of different modes, particularly mode 1 and mode 2, passing over variable bathymetry are investigated based on a new numerical scheme. The problem is idealized as interfacial waves propagating on two interfaces of a three-layer density stratified fluid system with large-amplitude bottom topography. The Dirichlet-to-Neumann operators are introduced to reduce the spatial dimension by one and to adapt the three-layer system and significant topographic effects. However, for simplicity, nonlinear interactions between interfaces are neglected. Numerical techniques such as the Galerkin approximation, proven effective in previous works, are applied to save computational costs. Shoaling of linear waves on an uneven bottom is first studied to validate the proposed formulation and the corresponding numerical scheme. Then, for two-dimensional numerical experiments, mode transition phenomena excited by locally confined bottom obstacles and quickly varying topographies, including the Bragg resonance, mode-2 excitation, wave homogenization, etc., are investigated. In three-dimensional simulations, internal wave refraction by a Luneberg lens is considered, and good agreement is found in comparison with the ray theory. Finally, in the limiting case, when the top layer can be negligible (for example, a gas layer of extremely small density), the problem is reduced to a two-and-a-half-layer fluid system, where an interface and a surface are unknown free boundaries. In this situation, the surface signature of an internal wave is simulated and verified by introducing the realistic bathymetry of the Strait of Gibraltar and qualitatively compared with the satellite image.