Herein, discipline decomposition was performed for an autonomous underwater vehicle (AUV) based on multidisciplinary design optimization (MDO), and its design parameters were determined. Parameterized analysis of the hull-form and structure disciplines was performed, and an approximate model of these disciplines was established with a high fitting accuracy. An analysis model of propulsion, energy, and system disciplines was developed based on the formula method. Based on collaborative optimization as well as discipline and system level models, a deterministic MDO framework for AUVs was established. Subsequently, an optimized solution was obtained. By considering the random uncertainty of design variables, an MDO framework for the uncertainty of AUVs was established and optimized solutions were obtained. The distribution of solutions obtained from uncertainty optimization was more concentrated and the distribution range was smaller than that obtained using deterministic optimization. Robustness analysis was performed on the initial scheme, typical deterministic optimization schemes, and typical uncertainty optimization schemes. Results showed that fluctuations in design variables may lead to constraints that exceed boundary conditions in the deterministic optimization design scheme. Using uncertainty and objective function optimization, the robustness of the overall scheme of AUVs was improved.