In order to reduce the risk and loss of ship failure, it is necessary to fully consider the influence of various uncertainties in the overall design. Therefore the ship uncertainty optimization design, including robust design optimization (RDO) and reliability-based design optimization (RBDO), has been developed. The key to the uncertainty design optimization is the uncertainty quantification (UQ). The commonly used Monte Carlo simulation (MCS) method is expensive in high-precision simulation, while the polynomial chaos expansion (PCE) method can be used to quantify the random properties of the output of the uncertain parameters with less computing cost, which is more advantageous than MCS method in engineering application. Therefore, this paper takes the ship uncertainty design as the research object, analyzes the influence of multiple random variables on the optimization target and the constraint, and proposes a ship uncertainty design based on the multidimensional polynomial chaos expansion method, finally applies it into the concept design of a bulk ship, to ensure the robustness and reliability of the ship.