Based on the construction foundation of the national first-class undergraduate major in Biotechnology and the national and provincial first-class courses of the college, and standing on the overall goal of cultivating high-quality interdisciplinary talents of the University of Jinan, this paper intends to explore the “333” Training System for Biomedical Innovative Talents featuring “Ideological and Political Education Integration · Digital-Intelligent Empowerment”. The first “3” refers to the “three-wheel drive”, which constructs the educational philosophy of “Ideological and Political Education for Moral Cultivation, Digital-Intelligent Empowerment, and Innovative Output” to drive the cultivation of three core attainments: “Patriotism and Social Commitment, Digital Awareness, and Innovative Spirit”. The second “3” denotes the “triple digital integration”, which establishes a digital transformation paradigm of “Platform-based Curriculum Teaching, Blended Teaching Mode, and Visualized Evaluation System” to promote the improvement of students’ autonomous learning ability. The third “3” represents the “tripartite collaboration”, which builds a tripartite collaborative education model involving “universities, enterprises, and society” to enhance the effectiveness of the “three-wheel drive” education. Through the above reforms, a replicable and promotable new paradigm for cultivating interdisciplinary innovative talents in biomedicine is formed.