Against the backdrop of the high-quality development philosophy and the Healthy China strategy, medical innovation and entrepreneurship education still face issues such as unbalanced training concepts, prominent disciplinary barriers, insufficient resource support, and inadequate exertion of counselors’ roles. Adopting a problem-oriented approach, this paper focuses on the empowering value of counselors in medical innovation and entrepreneurship education, and systematically explores their role reconstruction, competency adaptation, and implementation paths. The study points out that counselors should transform from traditional administrative managers to “innovation education hubs”, establish a corresponding competency system around three core roles, and propose a four-dimensional practical pathway consisting of “cognitive enlightenment, competency training, resource coordination, and project incubation”. This research provides actionable references for universities to optimize the medical innovation and entrepreneurship education system with counselors as the fulcrum, enhance the effectiveness of empowerment, and help cultivate high-level interdisciplinary medical innovative talents that meet the needs of high-quality development.