With the continuous advancement of the country’s construction of “new engineering disciplines” and the reform of professional degree graduate education, innovation and entrepreneurship education has become an important way to improve the quality of graduate training. Based on the survey data from the School of Mathematics and Physics, this paper systematically analyzes the main problems existing in the innovation and entrepreneurship education for professional degree postgraduates through questionnaires, interviews and other methods, including insufficient atmosphere, imperfect system, lack of willingness and ability, incomplete educational layout, and shortage of teachers and practice platforms. On this basis, it proposes a collaborative education model centered on the integration of “industry, teaching, research and application,” and puts forward specific countermeasures from the aspects of policy guidance, tutor team construction, integration of school-enterprise resources, and optimization of curriculum and teacher systems, so as to promote the all-round improvement of the innovation and entrepreneurship ability of professional degree postgraduates.