This study aims to optimize an arrangement of ship compartments with knowledge-based systems. Though great attention has been shown to the optimization of hull forms in recent years, the study on arrangement design optimization has received relatively little attention. A ship is both an engineering system and a kind of assembly of many spaces. This means that, to design an arrangement of ship compartments, it is necessary to treat not only geometric data but also knowledge on topological relations between spaces and components of a ship. In this regard, we select a suitable knowledge representation scheme for describing ship compartments and their relations, and then develop a knowledge-based system using expert system shell. This new approach is applied to create design variations for optimization on an arrangement of a pressure hull of a submerged vehicle. Finally, we explicate how our approach improves the design process.