| The innovation is the life line and the soul of regional economic development. In the regional innovation system, the research university should become important links of support; becomes the power support of national and regional economy development, the society progresses and the technical innovation; becomes the important base of the high new technical achievement shifting and the high new technical industry hatching; becomes the think tank, the knowledge library, the talented person storehouse and the achievement storehouse of national and regional innovation system; becomes the center of the stimulation of innovation thought, the dissemination of innovation culture, the cultivation of innovation talented person and the construction of innovation environment. At present, according to the overhead construction which the research and the non- research university unifies, we construct the national university system in the new century, this is the objective need of a better join of the research university and the national innovation system, the construction of regional innovation system, and the need of promoting our country's ability of independent innovation. This article combines Triple Helix of regional innovation system; the study shows that the research type university is the source of knowledge production, is the ligament of knowledge dissemination and the core of knowledge transfer in knowledge innovation; the research type university can form human capital and net of intercommunion, bring "knowledge overflow effect" to the development of whole region and participate in the dissemination and transfer of knowledge in cultivation of talented person. Bases on Triple Helix, the author introduce game theory analysis and discuss the function mechanism of the research type university in regional innovation system. The result shows that the cooperation and innovation of innovation main body exists obviously regional because of seeking expenses and the probability of cooperation from innovation main body and other innovation main body inside the region is bigger than the cooperation from innovation main body outside the region. Enterprises which close to university acquire latest technique of university more easily than those which are far off. The behavior of looking for partners of innovation main body is not only related to seeking expenses but also is related to industry, some organizes and fields which have correlative techniques and its proper characteristic of technique innovation which is high risk and high repay. Therefore cooperation and innovation appears regional characteristic; the probability of cooperation and innovation reduces with the increase of seeking expenses. If the expenses are too high, cooperation and innovation would not occur. Contrarily, if the expenses are too low, the regional characteristic of cooperation innovation will disappear automatically. The cooperation region of high repay is lager than the region of low repay, reducing seeking expenses and developing high-tech industry which is high repay is propitious to achieve cooperation and innovation. To some extent, it can explain why the cooperation and innovation in university-enterprise is not common in China, especially in the less developed region.This article also study on main mechanism of cooperation and innovation between university and enterprises and figure out that there is a universal model of cooperation which is entruster and deputizer in the relation of cooperation and innovation of university and enterprises. In this model, university depends on its intellective advantage and enterprises depend on their financial and commercial advantage. This type of cooperation is the main stream of cooperation between university and enterprises. In this cooperation, the sticking point is that the benefits of enterprises and the behavior of university is consanguineous relation. But enterprises can not control the behavior of university directly; furthermore, it is hard to supervising university. They can only influence the behavior of university indirectly through recompense. The consigner designs a contract in order to maximize their benefits under the conditions of restriction and compatible restriction of encouragement. This contract is the result of game and Nash equilibrium.In the commission-agent relation of the government and university, this study shows that it will be propitious to enhance the efficiency of technique innovation through introduce the appropriate encouragement mechanism and punishment mechanism.
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