Abstract: In the context of the innovation-driven strategy and civil-military integration, to analyse the collaborative innovation of civil-military integration is of great significance to promote the in-depth development of civil-military integration.Applying the innovation chain theory, make an in-depth analysis of the collaborative innovation of civil-military integration and put forward corresponding countermeasures and suggestions. It comes to the conclusion that there are some problems in collaborative innovation of civil-military integration, such as separation of military and civilian innovation system, unclear status of innovation subject, insufficient of collaborative initiative and imperfect of guarantee mechanism.From the perspective of innovation chain, the countermeasures and suggestions are promoted from three aspects, such as, collaborative innovation subject, collaborative innovation process and external guarantee mechanism respectively.