Military-civil combined innovation is the important method of modernization construction in our country. So it receives a great deal attention of the government at all levels. The paper studied the mechanism and problem of military - civil combined innovation in Chongqing that is the important Military - civil Combined area. On the basis of the above, some creative suggestions was given about the motivation system, competition and cooperation mechanism, restriction system, and some innovation model was set - up, such as a model of innovation depended on enterprise, model of innovation platform, model of military and civil service innovation.