Abstract: With the rapid development of China's economy,civil-military integration has risen to the level of national strategy. National Defense Science and Technology Collaborative Innovation Systemhasbecome the important objectives of? civil-military integration. Based on the realistic requirements of civil-military integration depth development,this paper illustrates the connotation of national defense science and technology collaborative innovation system,and? makes some systematically? analysis in top-level design,attempting to break the boundaries between national defense science and technology innovation system and civil science and technology innovation system,combing the process of national defense science and technology collaborative innovation,coordinating various related subjects,optimizing the allocation of resources in various fields,to meet the needs of the military and promote the innovation and development in the field of national science and technology. National Defense Science and Technology Collaborative Innovation System is combined with innovation system,innovation mechanism and innovation legal system,the integration is beneficial to the collaborative innovation in military and civil field,which is conducive to the leading role the government in the national defense science and technology collaborative innovation system,improving the efficiency of market allocation of innovation resources,and promoting the development of national defense science and technology.