Abstract: Modeling and simulation for a complex software prototyping system were computer supported cooperative work process. To effectively manage its business process and data and thus improve the efficiency of the whole system-s work, a workflow-based project management system was proposed. It was comprised by system management, project management, workflow management, document management, message management and information management. The hierarchical and modularized architecture and the components of this system were illuminated. Particularly, the workflow architecture, workflow modeling and running were thoroughly explained. The elements of the model and modeling mechanism included multi-instantiation, dynamic creating and revising of the workflow. Finally, the application of the project management to a virtual prototyping system for a weapon developing platform was introduced.