The research on innovation has become an important thread from the perspectives of system and its relative system theories. According to knowledge about regional innovation system and self-organization theory, the following viewpoints are put forward: (1)innovation integration is defined as a dynamic innovation process and system with a better comprehensive benefit in the times of knowledge economy, taking into account all perspectives of innovation, emphasizing harmony and match from all kinds of innovations, and all kind of innovations interacting with each other innovations such as culture innovation, knowledge innovation, institution innovation, technology innovation, management innovation and so on. (2)regional innovation integration is to realize the sustainable development of regional society and economy by means of the organic combination and dynamic optimization in regional all kinds of innovation (e.g. Culture innovation, knowledge innovation, market innovation, institution innovation, technology innovation, management innovation). And then the difference of all innovators engaging in innovations in regional innovation integration is expounded Based on analyzing the relationship among all innovators of regional innovation integration, the Self-organization model of regional innovation integration is set up and the matrix operation of the model is processed. The operation outcomes are received as follows: (1)there is no competitive effect, but synergetic effect when self-relation of single innovation in region acts on regional innovation integration. (2) if only self-relation of single innovation sub-system in region but lack of interaction among all innovation sub-systems, even if they themselves have effect, they will competitive and synergetic e not contribute to regional innovation integration. (3) The competition effect among the different innovation subsystems has active effect and passive effect, and the active effect has decisive influence on the final result of the regional innovation integration. (4) regional innovation integration by means of the interaction of innovation sub-systems, competition and cooperation under the situation that makes use of the resources in the innovation system, obtain ideal integrated result in the end, and will cause the birth of higher degree innovation integration, this explains the mechanism and its complex evolvement of self-organization about regional innovation integration well.
