Excellent engineers are strategic talents for the nation. Based on the idea of project-based governance and the theory of synergetics, a project-based model for school-enterprise collaboration aimed at cultivating excellent engineers is recommended, and combining the training practices of Southeast University's National College for Excellent Engineers. It elucidates its mechanisms from three dimensions: the project platform, the full process empowerment and control of university-industry collaboration, and the integrated development of knowledge, skills, and qualities. The research conclusions include that the establishment of the project platform provides an organizational structure for collaborative education through university-industry integration; the goal management and process control of project rationalization are realized, through the joint empowerment and risk management of schools and enterprises in the process of postgraduate training; the integration of industry and education in collaborative education helps to achieve the cultivation of knowledge and thought integration, as well as the cultivation of innovation ability and sense of responsibility. The project-based model provides a theoretical foundation and practical guidance for the cultivation of excellent engineers in the new era.