Traditional ship design management, centered on drawings and documents, suffers from prominent issues such as discontinuous design processes, scattered data carriers and low collaboration efficiency. To advance the digital transformation of ship design management, this paper constructs a whole-process management system for ship design that takes 3D models as the sole authoritative data source and bill of materials (BOM) collaborative integration as the core. This system covers seven key application scenarios including project management, plan management, review and verification management, submission and return review management, shipyard-institute collaboration management, model data management and archive management. All scenarios feature interlinked data and closely connected processes, forming an integrated whole-process management system. Combined with practical implementation in multiple ship-type projects, the application value of this system has been verified. The new digital design management model proposed in this paper effectively addresses the problems of data silos, version inconsistency and poor collaboration in traditional design management, providing a reference for ship enterprises in the construction of digital design management systems and facilitating their intelligent and digital transformation.