Because of its cross-organization, cooperative innovation project faces with more serious risk in team relationship. Through questionnaire survey, as well as the multivariate statistical analysis of over one hundred cooperative innovation projects in several fields, this paper revealed how positive team management can be embedded in relational governance in the cooperative innovation project. Positive team management can perfect the emergency ability which marked by particular position arrangements of teams, diversify the way of risk identification, early warning and disposing in task and relational conflict. Then cooperative innovation can determine the effective strategies in all kinds of relational governances, and make them more efficient in moderating working, emotional and moral relationships. Above all, not only they can motivate team creativity, but also be good for comprehensive performance of innovation projects.