In ship design optimization, uncertainties in design variables or operational environments may prevent the ship performance from achieving the optimal objectives under the design conditions, and even lead to drastic performance deviations, causing the original design scheme to fail. The uncertainty-based design optimization method has been introduced into the ship design in order to mitigate the influence of uncertainties on the ship performance and enhance the robustness and reliability of ship design schemes. A mathematical model for the ship design optimization under the influence of uncertainties is established, along with its corresponding solution process. This method is then applied to the design optimization of a bulk carrier. The optimization results show that compared with the deterministic optimization scheme, the uncertainty-based optimization scheme is superior, and its robustness and reliability have been significantly improved.