To develop an underwater vehicle with better propulsion performance allowing long-time observations in the ocean, the resistance force acting on the vehicle is accurately estimated using computational fluid dynamics (CFD) and experiments in a towing tank. The flow around the body is simulated by a commercial CFD code (STAR-CD), and actuation of the thruster is modeled by a simplified propeller theory. The two-way coupling between the flow and the thruster is treated with an iteration scheme to satisfy the condition of equilibrium between the resistance and the thrust. For validation of the numerical method, the resistance computed is compared to the one measured by the experiment, which turns out to be good in agreement. In addition, the optimization of the body shape for less resistance is studied by considering several body shapes with their self-propulsion factors taken into account.