Abstract:  The evolutionary game theory is applied to analyze the game behavior of limited rational government, military industrial enterprises and private enterprises from the dynamic angle, and the evolutionary stable strategy of both agents in the cooperation innovation system under the guide of the government is discussed, then optimal cooperation measures and suggestions are put forward. The results show that the excess returns, total cost, betrayal income and other factors have a direct influence on the strategy selection in the cooperation process. The government should create good civilmilitary integration development environment through the establishment of perfect incentive, supervision and punishment mechanism and play the role of macroeconomic regulation and control, and it can promote innovation system to achieve Pareto optimality.

Key words: military enterprises, private enterprise, government support, replicator dynamics, evolutionary stable strategy