The innovation networked organizations for the cooperation innovation of industries, universities and research institutes were classified into three types of organizations: technological coordination organizations, contracttype cooperation ones and integrated ones.  From the perspective of value chains, the process of the cooperation innovation was divided to two stages: R&D and the commercialization of its outcomes. A dynamic game model with complete information was set up according to the mature level of innovation ability, by which the way how to choose the paths of the cooperative innovation was discussed. The results demonstrate that the level of innovation ability impacts on the path choice as well as its evaluation.  An example of data simulation is also given.