Innovation and entrepreneurship education has become one of the important directions of higher education reform, but the innovation and entrepreneurship education in medical colleges and universities generally lags behind other disciplines or comprehensive colleges and universities. It is of great significance to explore a suitable talent training mode of the integration of innovation and entrepreneurship education and medical professional education. This paper summarizes the practical difficulties of medical colleges and universities' Entrepreneurship and innovation education, including the poor connection between entrepreneurship and innovation education and professional education, the imperfect curriculum system of entrepreneurship and innovation education, the weak construction of teachers, the weak awareness and motivation of medical students' Entrepreneurship and innovation, the imperfect system of entrepreneurship and innovation education, and the imperfect evaluation and assessment system of entrepreneurship and innovation activities. Based on the perspective of "triple helix" theory, this paper puts forward the strategy and practice mode of the integration of entrepreneurship and innovation education and professional education in medical colleges. The integration of entrepreneurship and innovation education in professional education aims to improve the entrepreneurship and innovation ability and comprehensive quality of medical students, improve the training quality of medical students, and better adapt to the needs of economic and social development.