In the process of movement, the submarine inevitably involves free surface navigation, such as floating observation, suction power generation, and rescue. Under various circumstances, the interaction between the submarine and the free surface leads to complex flow fields and wakes, which affects its hydrodynamic performance. In this study, a three-dimensional numerical model of a submarine considering the influence of free surface is established. The volume-of-fluid model with an artificial compression term is used to capture the gas–liquid interface, and the unsteady flow field and hydrodynamics are predicted using the shear stress transport k–ω turbulence model. Based on the analysis of mesh convergence and numerical reliability, the hydrodynamic performance and wake flow field characteristics of submarines under different submergence depths were studied. The results show that the free surface has a significant influence on the resistance, wave wake, wake field, and vortex structure of the submarine, which is closely related to the submergence depth. Compared with the infinite submergence depth, the total resistance of the submarine near the free surface increases by 159.2%, mainly due to the pressure resistance. The surface wave system generated by the interaction between the free surface and the hull will directly affect the distribution of the wave surface wake, the wake flow field, and the vortex structure. As the submergence depth increases, the free surface effect gradually weakens, and it can be ignored when the submergence depth is more than 4 times the diameter of the hull.