Abstract:This paper studies the application of evolutionary game method under the assumption of bounded rationality, the introduction of additional income distribution coefficient, the amount of liquidated damages penalties and other factors, structural Cooperative Innovation evolutionary game model and numerical simulation matlab conducted to determine the evolutionary strategy stability analysis of the production side and the strategic choice behavior Gakken parties. The results show that: the result has a distinct evolutionary "path dependence" feature, depending on the initial state of the system and how much income and gains derived from cooperation with partners can get a fair amount of punishment is closely related to the allocation and liquidated damages. Therefore, to determine a reasonable amount of liquidated damages to punish, and the best allocation ratio, in order to ensure convergence to the steady state of both production and research cooperation.