A heavier-than-water underwater vehicle (HUV) is unlike an unmanned underwater vehicle. The most notable characteristic is its ability to balance its weight with the hydrodynamic lift of water even though the weight is much greater than the buoyancy. Since the hydrostatic equilibrium is not based on the balance between the gravity and the buoyancy, the vehicle has a smaller volume, a larger payload, and better maneuverability. However, the design of the vehicle relies heavily on the abilities of naval architects. In order to ease the reliance on naval architects and to improve the prototype design, we propose a multidisciplinary system model using a semi-empirical model and three multidisciplinary design optimization methods. We applied all-in-one method, analytical target cascading method, and bi-level integrated system collaborative optimization method to the conceptual design of the vehicle in order to attain an optimal multidisciplinary design characterized by minimal total weight, long-range cruising capabilities, and high maneuverability. The results from the three different methods show that the general performance of optimized HUV was significantly better than the performances of prototype design, which suggests the feasibility and superiority of model and optimization methods.