For the intellectual property risk, the scholars were mainly studying the legal conflict of intellectual property faced by enterprises from the perspective of law, and relatively few researches were conducted on risks of intellectual property from the viewpoint of management in-depth study. In view of this, through analyzing the relationship of knowledge potential difference between the enterprise and the research party in the process of cooperation, the paper studies the intellectual property risks in the cooperation. The process of cooperative governance is introduced as a critical variable to construct a theoretical model exploring relationship among knowledge potential, intellectual property risk and two dimensions of cooperative governance. Then 213 questionnaires were collected and analyzed to verify our hypotheses. Statistic analysis shows knowledge potential difference has a significant effect on the risk of intellectual property; cooperative governance has different influence on the risk of intellectual property in terms of its two dimensions; cooperative governance also plays a moderate role in the relationship between knowledge potential and intellectual property risk.