The preliminary design stage for a naval surface ship requires several performance parameters to be considered, including stability, operability, and survivability. These parameters have to be considered for many compartments constrained by a limited space, so this problem is complex and with many possible design alternatives. However, the arrangement during the actual design of a ship depends heavily on having experienced designers and parent ships. There is no mechanism to quantitatively evaluate the arrangement design. For these reasons, the probability of changes in the design increases as the design progresses.This study proposes a method to arrange a naval surface ship while considering the stability, operability, and survivability, and a prototype program based on the proposed method is herein developed. First, a template model is defined consisting of a data structure to represent the arrangement information of the ship. Second, methods are studies to quantitatively evaluate the stability, operability, and survivability of the ship, by referring existing studies. Third, two-stage optimization problems for the arrangement design are mathematically formulated, selecting design variables, objective functions, and constraints. Finally, a user interface is developed to input the given data and to output the optimization result for the arrangement design. The applicability of the proposed method is verified by implementing an example of a 7000-ton class missile destroyer. The result shows that the proposed method can be effective in producing better alternatives for the arrangement design during the preliminary design stage.