In order to solve the difficult physical problem of moving structures through free surface and stratified fluid interface, the paper presents and develops a new method based on surface capturing method and Cartesian cut cell mesh to handle transient density interface and moving boundary. Therein, quad-tree data storage structure, adaptive grid techniques, and high-resolution reconstruction limiter are introduced to improve computational efficiency and precision. Hybrid mesh systems of structural and Cartesian cut cell mesh are extended to be applied in the laminar flow problem at low Reynolds number. On this basis, a series of experimental tests of cylindrical models falling through air-water, air-oil and oil-water interfaces are carried out respectively, then several cases are taken to validate the numerical method. Sequentially, the characteristics of interface variation and closure shape versus different density ratios are compared, and the effect of stratified fluid interface on the hydrodynamic force of moving body is mainly discussed. In summary, this paper unifies free surface and stratified fluid interface together as density interface, which can be handled and studied by the same numerical method. Thus, by combining water entry with stratified fluid problem, the influence of various density interfaces on moving body can be better analyzed.