Abstract Hightech industry has become the main force to promote economic development. As the main power to improve the development of hightech industry, innovation is more and more important. In this paper, based on the importance of hightech industry in economic development and theory of synergetics, the structure of the hightech industry collaborative innovation system have been analyzed, through which the innovation entity subsystem and innovation environment subsystem have been recognized. After the influencing factors have been analyzed, casual loop diagram and system flow chart have been drawn. With JingJinJi as the example, five simulating schemes have been designed using the software of Vensim. According to the results of simulation, some countermeasures to improve the collaborative innovation ability have been put forward.