Against the backdrop of the “Transportation Power” strategy and the accelerating shift of the rail transit industry toward intelligence and system integration, there is an increasingly urgent demand for high-level graduate talent equipped with engineering innovation capabilities and systems thinking. This paper focuses primarily on training master's students in the urban rail transit industry and on cultivating innovation capabilities in doctoral students. In response to prominent issues in current graduate education—such as insufficient adaptability of the curriculum, weakened interdisciplinary integration, and inadequate industry–education collaboration—this study develops and proposes an innovative graduate training model characterized by “three pathways, four stages, and three strategies.” This model adopts the deep integration of “curriculum–research–practice” as the primary training pathway, structures a closed-loop process for innovation capability development through “problem identification–solution design–scenario validation–outcome consolidation,” and implements supporting strategies via “dynamic curriculum updates–university–industry platform co-construction–contribution-oriented evaluation.” By optimizing course clusters targeting cutting-edge fields such as intelligent operation and fully automated systems, reinforcing research training within real engineering scenarios that couple multiple disciplines, establishing an evaluation mechanism guided by contributions to solving practical industry problems, and integrating university–industry collaborative practice pathways, the model forms a feasible training and assessment system that systematically promotes the transformation of graduate students’ innovative abilities from “knowledge acquisition” to “engineering creation.” The study concludes that this model provides a valuable reference for enhancing graduate students’ engineering innovation abilities and comprehensive competencies, offering significant implications for reference and broader application in cultivating innovative talents within the rail transit industry and related engineering domains.