In order to further strengthen the performance management of the Beijing innovation team of modern agricultural industry technology system, this article is based on the questionnaire survey which involved in all members of the Beijing innovation team. Using the PCA method to analyze the factors which influence the performance management of Beijing innovation team, studying out system design and management, goal-management, members' competence, members' quality and process management are the key factors to influence the performance management. The system design and management is the most important factor, followed by the consistency of objectives, members of competence, again is the quality of the members and daily management. According to the role and problems of various factors, proposing some policy suggestions to improve team performance management, for example, perfecting the team system design, setting clear goals, establishing effective communication mechanism, strengthening the construction of team members’ quality and so on.