Abstract: The innovation level of central universities is outstanding. The influence of local universities is growing. Industry-University-Research cooperation is becoming more and more important in China's innovation system. Different types of universities and industry-university -research cooperation play a specific role in China's innovation system. How do these different roles operate in China's innovation system, what is the operating mechanism of China's scientific and technological innovation, and how do they affect the technological progress of the whole society? These are worthy of further exploration by researchers. Clarify the important significance of Industry-University-Research cooperation for university innovation, reveal the heterogeneity of the roles of different types of universities in the innovation chain, provide targeted suggestions for the classified development of China's higher education, and provide enlightenment for optimizing the operation of each link in China's innovation chain. This will contribute to the further development of China's higher education and promote China's scientific and technological progress. From the perspective of innovation chain, the research fully considers the differences between central universities and local universities, brings the Industry-University-Research cooperation, scientific and technological innovation of different types of universities and technological progress of the whole society into the innovation chain, and puts forward three assumptions H1, H2 and H3 to build a theoretical model. Using the panel data of 31 provinces in China for 10 years, this paper calculates the total factor productivity to reflect the technological progress of the whole society, and applies the intermediary effect model and the fixed effect panel regression model to empirically study scientific and technological innovation process of different types of universities and influencing factors of technological progress respectively, and hypothesis tests are conducted on three theoretical hypotheses H1, H2 and H3, so as to reveal the operating mechanism of scientific and technological innovation in China's innovation chain. Finally, the study accepted the H1, H2 and H3 hypotheses. It is found that there is heterogeneity in the scientific and technological innovation mechanism between local universities and central universities. Strengthening the cooperation between industry, universities and research institutes is of greater significance to the central universities. Increasing investment in innovation will be more beneficial to local universities. Among the various influencing factors of technological progress in the whole society, the role of different factors is heterogeneous. The role of high-tech industries is distorted. The central universities have a significant positive effect. Put forward some suggestions: it is an important path to promote the innovation of local universities to increase the innovation investment in an extensive way. Central universities should strengthen cooperation between industry, university and research institute, promote the transformation of scientific and technological achievements, improve the mechanism of Industry-University-Research cooperation, change the extensive development model and take the road of fine innovation. The high-tech industry needs to constantly straighten out the innovation chain, improve the innovation mechanism of the high-tech industry, and gradually reverse the distorted technological impact of the current high-tech industry. The technological progress of the whole society needs to give full play to the leading role of the central universities. Various measures should be taken to support the development of central universities in order to promote the technological progress of the whole society.