Civil-military inosculation of military enterprises benefits national defense industries by promoting the building of civil-military inosculation innovation system. To analyze the operation mechanism of the civil-military integrated innovation system of the military enterprises under the new situation,the system dynamics method is used to study the feedback relations among the factors and structure of the system and the Anylogic software is used to establish the simulation model . The simulation results indicate that: the degree of enthusiasm of private enterprises to participate in the defense industry,the degree of information sharing and the degree of cooperation between the military enterprises and universities and research institutions are extremely important in the civil-military integrated innovation system. According to the simulation results,some targeted suggestions are put forward to strengthen the innovational civil-military integrated system building of the military enterprises. Civil-military inosculation of military enterprises benefits national defense industries by promoting the building of civil-military inosculation innovation system. To analyze the operation mechanism of the civil-military integrated innovation system of the military enterprises under the new situation, the system dynamics method is used to study the feedback relations among the factors and structure of the system and the Anylogic software is used to establish the simulation model. The simulation results indicate that: the degree of enthusiasm of private enterprises to participate in the defense industry, the degree of information sharing and the degree of cooperation between the military enterprises and universities and research institutions are extremely important in the civil-military integrated innovation system. According to the simulation results, some targeted suggestions are forward to strengthen the innovational civil-military integrated system building of the military enterp rises.