Innovation and entrepreneurship education in colleges and universities helps enhance college students" comprehensive understanding of entrepreneurship and serves as an important link between university professional learning and industrial practice. Innovation and entrepreneurship education in specialized type institutions, under the goal orientation of cultivating entrepreneurial intentions, particularly needs to forge an innovation and entrepreneurship education curriculum system that conforms to its own characteristics. This paper collects data from 1,209 students in 41 public medical undergraduate institutions in 27 provinces (autonomous regions and municipalities directly under the Central Government) across the country to explore the relationship between the depth and breadth of innovation and entrepreneurship learning, autonomous learning motivation and entrepreneurial intentions among medical college students. The research results show that the depth of innovation and entrepreneurship learning has a significant positive impact on entrepreneurial intentions; the breadth of innovation and entrepreneurship learning has a mediating effect in the relationship between learning depth and entrepreneurial intentions, and autonomous learning motivation has a positive moderating effect in the relationship between learning depth and entrepreneurial intentions. The results of the heterogeneity study indicate that the depth of innovation and entrepreneurship learning is more likely to stimulate the entrepreneurial intentions of male, urban-hukou and non-medical major students in medical colleges. The research conclusions are helpful for colleges and universities to further improve the design of innovation and entrepreneurship education courses and policy optimization, and enhance the entrepreneurial intentions of medical college students.