To investigate the influence of different navigation parameters on the wave-making characteristics of submarines navigating in deeper density layers, based on viscous-flow theory, a multi-phase flow numerical model with user define function to specify the distribution of different fluid layers is established for analyzing the hydrodynamic characteristics of the submarine navigating in density-stratified fluid. The wake characteristics of the submarine navigating with different forward speeds and submerged depths in deeper density layer, which means the navigating position below the interface of internal wave, are numerically simulated. And the discussion is carried out by analyzing the results of wave profile, fluid-velocity distribution and wave pattern. The results show that the forward speed has a remarkable effect on the wake of the navigating submarine in the deeper density layer. The most significant wake on the bow and stern of the submarine is noticed when the submarine is advancing at a the mid-speed stage near Fr＝0.6. The submerged depth of the submarine affects the wave amplitude on both the free surface and the internal surface. Compared with the submarine navigating in the shallower density layer, the wave-making characteristics on free surface generated by the submarine navigating in the deeper density layer are similar, but the internal surface wake is significantly different. The change of the fluid-velocity distribution on the interfaces with different navigation parameters is consistent with the change of the wave-making characteristics. Revealing the characteristics of wave-making of submarines when navigating at a special position in the deeper density layer can enrich the analysis methods of hydrodynamic characteristics of navigating submarines at different positions, and provide a reference for submarine non-acoustic detection.