In the environment of a new era that growing nation with science and technology, innovation and entrepreneurship education for college students has been continuously promoted. 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, firstly, 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 was presented. Secondly, taking the second classroom system of Shandong Jianzhu University as an example, the evaluation system characteristics and improvement direction of the innovation and entrepreneurship education were analyzed. Meanwhile, the path of multi-subject innovation and entrepreneurship education under the university-enterprise cooperation mode was described. Based on the education and training reform under the mode of university-enterprise cooperation, the innovation and entrepreneurship platform of the school was developed in diversified directions. And the Students' innovation and entrepreneurship ability was improved. The multi-subject university-industry cooperation mode of entrepreneurship and innovation got the 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.