Starting from the basic definition and connotation of collaboration of industry-university-research and collaboration innovation, this paper gives detailed analysis of the two matters, both on their common points in terms of functional role, theoretical basis, organizing body, participants and focal issues; as well as on their differences in terms of innovation focus, collaborative methods, range of participation, emphasis on problem-solving, entity and other aspects. Thus, concluding and illustrating the importance and primary methods of how to combine the two, so as to create innovative talent cultivation mechanism and effective structure of academic and scientific research.