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In order to get an acceptable interests-distribution scheme for each partner of enterprise-university-research institute cooperation in advance, based on Nash model, the paper designs the interest distribution method of enterprise-university-research institute cooperation and provides the basis for determining the weight of each partner in accordance with the interest distribution principles and subjected relations between major factors in enterprise-university-research institute cooperation. Also, in combination with one example, an applicable method is provided to distribute interest in enterprise-university-research institute cooperation. The study gives some references for interests-distribution of enterprise-university-research institute cooperation.