The strategic alliances of industry-university- research institute is senior form of industry-university- research institute collaboration,it is a important mode to drive the innovation of science and technology and strategic competition for all the countries in today's world. In order to make the strategic alliances of all parties seek harmony among the multiple conflicts ,it is necessary to establish the win-win mechanism of the strategic alliances of industry-university- research institute from the point of view of the system.This paper starts from the construction and operation process of the stategic alliances , discussing and analysising the eight kinds of win-win mechanism of the strategic alliances of industry-university- research institute that are respectly the selection and exit mechanism、the division of labor and collaboration mechanism、the organization and coordination mechanism、the incentive and constraint mechanism、 the benefit sharing mechanism、the risk sharing mechanism、the supervision and evaluation mechanism and the information sharing mechanism.