Abstract:Civil-military collaborative innovation involves complex multi-subject, and its interest distribution, long-term incentive and compensation mechanism are still restricting the participation enthusiasm of civil-military collaborative innovation subject. First carries on the definition of collaborative innovation through the joint efforts of the compensation incentive mechanism, analyze the necessity of compensation incentive mechanism, build military and civilian collaborative innovation building including compensation incentive compensation principles, compensation incentive subject, object, type of compensation incentive compensation and a series of system arrangement of the military and civilian collaborative innovation incentive mechanism, and to "Tianhe no.1" super computer dual-use technology collaborative innovation compensation incentive mechanism used for case analysis. Finally put forward policy Suggestions to perfect the collaborative innovation through the joint efforts of the compensation incentive mechanism,.