In the background of building a country of technological power in the new era, it is necessary to continuously promote innovation and entrepreneurship education for college students. The school-enterprise cooperation mode becomes a new mode of innovation and entrepreneurship education between universities and enterprises, with the significance of deepening integration of industry and education. In this study, according to the characteristics of the training of innovative and entrepreneurial talents in science and engineering universities, the current innovation and entrepreneurship education training system is presented. Taking the second classroom system of Shandong Jianzhu University as an example, the characteristics and improvement direction of the evaluation system of innovation and entrepreneurship education are analyzed. Meanwhile, the path of multi-subject innovation and entrepreneurship education under the university-enterprise cooperation mode is described. Based on the education and training reform under the mode of university-enterprise cooperation, the innovation and entrepreneurship platform of the school is developed in diversified directions, and students’ innovation and entrepreneurship ability is improved. The multi-subject university-enterprise cooperation mode of entrepreneurship and innovation gets beneficial effects. The path analysis and practical exploration of innovation and entrepreneurship education will provide reference for the construction of innovation and entrepreneurship education in science and engineering universities.