Industry-University is one of the core contents of our national innovation strategy, and now it has developed to the phase of synergy. The synergy efficiency of industry-university is low, which is not enough to realize the ordering of the structure of industry-university. The idea and method of reciprocity is one of the power sources to activate the cooperation of industry-university. The empirical results show that the reciprocal cooperation and interaction have significant promoting effects on the quality, market adaptability and input-output matching of the industry-university projects. Our country should take the path of reciprocal cooperation, cultivate reciprocity culture, learn from western reciprocal experience, solve incomplete contract problems with reciprocal cooperation, drive honest cooperation with reciprocity, and abandon extreme egoism in cooperation and flexibly implement cooperation system and norms, through which we can break through the bottleneck in the collaborative innovation of industry-university.