Because the ocean exhibits different stratification states in different seasons and regions, the effect of different stratification parameters on a submarine wake must be studied. In particular, to investigate such effect in a two-layer stratified flow, this study established a computational fluid dynamics (CFD) model based on the URANS equations, shear-stress transport (SST) k-ω turbulence model, and Eulerian multiphase flow model. The volume of fluid (VOF) method was adopted to implement the free-surface capture method. The working conditions of the SUBOFF model under an infinite diving depth and near the free surface were compared with those of the experiments, and the convergence of the time step and grid number under stratified flow conditions was verified. These validation steps proved the feasibility of the CFD method. Finally, the effects of the stratification parameters on the free surface waves, internal waves, and turbulent kinetic energy behind the vehicle were observed by varying the stratification parameters to achieve different working conditions. The results show that when an underwater vehicle sails in a two-layer stratified flow, the interstratified density ratio and depth of the internal wave surface affect its wake field. When the underwater vehicle sails in the water layer, with an increase in the interstratified density ratio, the free-surface roughness increases and the turbulent kinetic energy decreases. When the underwater vehicle sails in the salt water layer, the result is just the opposite.