Abstract: In this paper, based on the theory of innovation chain, we propose a method to identify potential industry-university-research institutions cooperation partners, combining with the theory of enterprise competence. Firstly, we put forward the theoretical assumptions of potential cooperation partner recognition, according to discrepant competence among institutions in innovation Chain. Secondly, using multi-source data and qualitative and quantitative analysis, we do research on the multiple mode of enterprise-university-research institute cooperation and layout features of competence in innovation Chain. Then, according to the principle of competence complementarity and the previous hypothesis，we try to identify potential cooperation object. Finally, we verify the feasibility of the method by an empirical analysis in the field of gene engineering vaccine. The results show that: through the analysis of discrepant competence among institutions in innovation chain, we can effectively identify the potential cooperation objects.