Abstract: Cooperative innovation has the advantages of realizing resource complementarily, reducing the risk of innovation and improving the possibility of innovation success, but it is difficult to maintain the stability of cooperation among enterprises in practice. Because the behavior of innovators directly affects the stability of cooperative relationship, the research on the behavior of innovators has always been one of the focuses. However, most of the existing studies are based on the assumption that the innovators are completely rational. Obviously, there is a gap between this assumption and the reality. In view of this problem, based on the hypothesis of bounded rationality, the traditional expected utility theory is changed, introduces the reference dependence is introduced to analyze the utility of the innovation subject, and the cooperative innovation revenue matrix. Based on the matrix is constructed, the evolutionary game analysis of the cooperative game is carried out, and the numerical analysis is simulated by MATLAB.
The research shows that the factors such as the perceived value of cooperative innovation and independent innovation, the cost of cooperative innovation, the distribution of income are the important factors affecting the stability of cooperation. It is beneficial to enhance the stability of cooperation and innovation by enhancing the perception of long-term strategic cooperation and innovation and guiding enterprises to establish correct innovation risk awareness and controlling the transaction cost of cooperative innovation.
The interaction of cooperative innovation subjects in the context of bounded rationality is examined, and corresponding policy recommendations are given to enhance the stability of cooperative innovation on the analysis of game analysis, which is helpful to expand the research of bounded rationality in the field of cooperative innovation.

Key words: cooperative innovation, reference dependence, prospect theory, evolutionary game, bounded rationality