In the era of digital transformation, to address uncertainty, improve quality and efficiency, and enhance enterprise profitability, integrating digital technology into ship design technology to reconstruct a full three-dimensional (3D) ship design model has become a design development trend. A model-based integrated 3D digital design definition and technical connotation are proposed by using Hexagon Smart 3D as the 3D design platform. The solutions for 2D-driven 3D rapid modeling, integration of CAD/CAE, integration of detailed design and production design, 3D submission for approval and design tool development are also discussed. A number of design tools are developed based on parametric modeling and knowledge-driven approaches, forming a modeling strategy and design master schedule (DMS). This addresses the integration of CAE/CAD and the integration of detailed design and production design, enabling the share and reuse of the unified data sources and model data, as well as the 3D design collaboration among various design departments. The research results have been applied in merchant ships and cruise ships, laying a solid foundation for reconstructing the fully 3D design model of ships.