Under the background of new-era technological development and the implementation of national strategies, an increasing number of national major scientific and technological infrastructures led by universities have come into operation. How to take the advantages of national facilities to serve major scientific researches while fostering innovative graduates has become an important issue in recent studies. Taking Shanghai Jiao Tong University as an example and building upon the first National Facility for Translational Medicine (Shanghai), this paper focuses on the cultivation of graduates' innovative research and practical abilities, constructs a three-dimensional collaborative education system of "institutional empowerment-knowledge transfer-capability forging, " and explores the implementation pathway through which national major scientific and technological infrastructures empower innovative talent development. Practice has demonstrated that converting the research and technological advantages of national major scientific and technological infrastructures into high-quality educational resources yields remarkable outcomes in empowering innovative talent development, offering a replicable paradigm for universities to enhance the quality of innovative talent cultivation through national multidisciplinary cross-cutting science and technology platforms such as national major scientific and technological infrastructures.