Based on the analysis of existing collaborative innovation research,according to the function of the innovation subject, the paper divides the collaborative innovation system into university collaborative inno- vation system and enterprise innovation system, and then constructs the collaborative innovation system model. The “Three-wheel-driven” school cooperative innovation system was constructed, and three-dimensional enterprises innovation system was built. The paper builds a collaborative research innovative coupling system, including technical storage,project cooperation,school-enterprise research platform, school locality innovation platform. It promotes school-enterprise in-depth collaborative cooperation actively, and then makes an empirical analysis with NUAA and Wuxi Enterprise Collaborative Innovation as an example.