Improving Military and civilian integrated innovation is one of core goals of the strategy of civil-military integration. According to the Game analysis of the enterprise innovative capability, choosing the integrated innovation between military - civilian enterprises is the optimum strategy of the “competition-cooperation” Game analysis. Based on Theory of Dissipation- Structure, we build structure、function model of military-civilian integrated innovation and complicated system model of military-civilian integrated innovation based on military - civilian enterprises innovative-body ,combining quantitative analysis, to investigate basic conditions of orderly evolution of military-civilian integrated innovation system. Finally, based on the theory of dissipation- structure perspective, we propose some revelation, that could make the operation of military-civilian integrated innovation system more effectively.