Industry-university-research collaborative innovation not only contributes to the flow of knowledge within the national innovation system, but is also a basic way to enhance the country's industrial technological capabilities. Aiming at the problem analysis of the collaborative innovation of industry-university-research institutes, drawing on the experience of deep integration of industry-university-research institutes abroad, the mechanism innovation from collaborative innovation of industry-university-research institutes to deep integration is proposed: The government should play an effective guiding role, give play to the role of the market in resource allocation, build a reasonable rights and interests distribution mechanism, build a value dimension of common development, and establish a joint talent training mechanism. Through the research of this topic, an innovation and entrepreneurship mechanism that is conducive to the transformation of scientific research results is constructed, and the relationship between universities and the government, industry and various innovation and entrepreneurship institutions is rationalized. Establish a benign interactive service management system, cultivate innovative and innovative talents, promote the aggregation of innovative elements, stimulate innovation potential, and promote the deep integration of technology and economy.