Abstract:In the collaborative innovation of enterprises, colleges and institutes, the enterprise (production side) is generally in a dominant position, and the hypothesis of research is based on selfishness. This paper introduces fairness preference theory, builds the profit distribution model in collaborative innovation of enterprises, colleges and institutes based on horizontal fairness and vertical fairness concerns, and the models in different states of information symmetry and information asymmetry are analyzed. The results shows that profit allocation model under the leading of enterprise is primarily affected by vertical preference. And along with the increase of fairness preferences of university and research institute,the increase of enterprise output and output sharing shows the effectiveness of the fair preference for collaborative innovation distribution of benefits. Synergistic benefits can assign real innovation can play a reference value. It can be used for distribution of collaborative innovation interests in reality, and play a reference value.