Against the backdrop that doctoral training for the professional degree in Civil and Hydraulic Engineering at universities is still largely oriented toward academic research and lacks sufficient depth in industry–education integration, this study—leveraging the institutional positioning of serving China’s national transportation sector and corresponding industrial strengths—proposes a project-based training mode framework for Civil and Hydraulic Engineering doctoral students in transportation industry universities. A synergistic linkage mechanism is established under the project-based approach, featuring five coordinated elements of talent cultivation: admission, funding, team, outcomes, and employment. With projects as the core carrier and through university–enterprise collaboration, the integration of the industrial chain, innovation chain, training chain, and value chain is strengthened, thereby promoting the alignment and integration of talent-training projects with scientific research projects and improving the quality of doctoral education for the professional degree in Civil and Hydraulic Engineering. Finally, the preliminary outcomes, effectiveness, and practical experience of implementing this project-based training mode are summarized and analyzed. The findings provide a useful reference for the cultivation of engineering doctoral students in similar universities.