Abstract: Innovation Consortium is an important factor to build the national innovation system. However, the diversity of stakeholders and the complexity of their interest demands lead to inevitable conflicts of interest in innovation collaboration, thus increasing the difficulty of interest integration and equilibrium, and affects the development of the Innovation Consortium. Therefore, this paper applies conflict theory and game theory to analyze the essence and mechanism of the conflict of interest in the Innovation Consortium, summarizes and brings up three types of conflicts: rule-based interest conflicts, relational interest conflicts, and distributive interest conflicts. Then, using theoretical methods such as multilateral bargaining game theory, normal distribution function, Shapley value method to construct a mathematical model of the interest distribution process of the Innovation Consortium, quantitatively evaluates various conflicts of interest in different parts of the process, and opting for a typical case to testify to the theoretical analysis. Finally, the paper puts forward some suggestions on how to balance the interests of all parties in the Innovation Consortium, including establishing an effective governance structure conducive to joint governance, promoting the construction of the culture of innovation, which has a core of enhancing mutual trust, as well as strengthening incentive and constraint measures based on dynamic management.