This paper uses the micro-survey data of the strategic emerging industry enterprises in seven provinces and cities from 2012 to 2013 and establishes the logistic regression model, in order to analyze the heterogeneity of cooperative modes and influential factors of industry-university-institute cooperation. The research results show that industry-university-institute cooperation is influenced by the enterprise's technological innovation factors, structure factors and environmental factors. Among them, technology innovation factors are most important. Considering industry-university cooperation and industry-institute cooperation respectively, we further found the differences of two cooperation models and influential factors: industry-university cooperation is positively influenced by the R&D intensity and ownership structure, while industry-institute cooperation is positively affected by the innovation performance and government tax incentives. Furthermore, the influential factors of different cooperation forms are also not identical. The form of cooperative R&D, technology transfer and advisory services are significantly influenced by technological innovation factors. Finally, we deeply analyze the main conclusion and present policy implications.