The integrated design of the ship form is a key issue in the design of submersible surface ship (SSS). In the simulation-based design (SBD) framework, lack of sample data leads to uncertainty in the surrogate model. In this paper, first, a hull cross-section shape modification technology, the self-fusion method, was used to change the ship form, and a fourth-order response surface model was introduced to establish surrogate model of hydrodynamic performance. Second, total resistance in the surface condition and one at a diving depth of 0.48 m were selected as the optimization targets. Third, an automated computing platform was developed to integrate the modules to improve computing efficiency and accuracy. Finally, to explore the adaptability of the ship form scheme, the interval optimization analysis method was introduced into uncertainty optimization. Among them, the interval variable was the surrogate model accuracy, and the targets were the minimum median and the minimum radius of the weighted resistance of cross-domain cases. A two-layer nested optimization system was chosen. Results show that resistance of the optimal SSS was reduced. The interval optimization results were compared with the deterministic optimization results, and the feasibility of hull shape interval optimization was verified.