A numerical model is developed to investigate the hydrodynamic characteristics of a moving submarine induced by internal solitary waves (ISWs) in continuously stratified fluids. A new numerical scheme for the generation of ISWs with a current is proposed, in which the forward speed of the submarine is equivalent to the current. The superposition of the velocity field obtained from extended Korteweg-de Vires (eKdV) theory and the velocity field of the current is taken as the initial velocity field in a numerical wave tank. Convergence analysis is conducted, while the present numerical model is validated by comparing it with experimental data. Then, the interaction between the moving submarine and the ISWs against different pycnocline thicknesses and different moving speeds is investigated. The proposed numerical model can produce accurate ISWs coupled with a current. It can be found that the hydrodynamic forces on the submarine decrease with the increment of pycnocline thickness. The moving speed of the submarine performs a significant effect on the horizontal force, but a light effect on the vertical forces and the torque. It is also found that the forces on the moving submarine cannot be considered as the linear superposition of the navigation resistance in still water and the forces induced by ISWs.