To study the wave-making characteristics of a shallow navigation submarine in the stratified fluid caused by density difference, a multiphase-flow CFD model for evaluating the wave-making characteristics is established by using the RANS equation, Realizable k-ε turbulence model and UDF method. Thereafter, the process of a full-appendage submarine navigating at different positions with low, medium, and high forward speeds in the shallow layer of density-stratified fluid is simulated, and the effects of the forward speed, the distance from interfaces and density-stratified fluid on the wave-making and velocity characteristics of the submarine in the interfaces are investigated. The result shows that the higher the forward speed and the closer to the interface are, the more intense the submarine wave-making in the interfaces will be. Especially in the mid-speed stage, there will be a large wave excited by submarine, and a big difference of wakes between the free surface and internal wave surface is obviously seen, of which the main performance is that the front of wave on free surface is a peak and the front of wave on internal surface is a trough. The response of the wave-making on the internal interface to the changes of various navigation parameters is insensitive than that on the water-free surface. The present numerical model has high accuracy, which can provide an effective method for analyzing the wave-making characteristics of submarine navigating in density stratified fluid.