How to give full play to the positive function of constructive conflicts (task conflicts and process conflicts) in the science and technology innovation team, give appropriate stimulation, mobilize the enthusiasm of employees and improve the team’s innovative ability to improve team performance and organizational effectiveness are issues that deserve both team leaders’ and scholars’ attention. Through selecting multiple medical technology R&D personnel from a specific science and technology innovation team of health organization, the research studies the constructive conflicts among the members of the science and technology innovation team, constructs and analyzes the conflict evolution game model, proposes countermeasures and suggestions for improving the innovation ability of the science and technology innovation team and discusses the innovation management mechanism of the science and technology innovation team. The study shows that task conflicts, process conflicts and innovation game decisions cannot be avoided. The unstable choice of members does not promote innovation. However, on the one hand, constructive conflicts can be controlled to maintain a moderate state of control. On the other hand, it is also necessary to establish a mutually trusting communication environment and convenient communication channels in the science and technology innovation team, combined with modern information management technology, to handle the problems that were difficult to be found or accumulated for a long time under the previous management mechanism and cooperate with the science and technology innovation team to improve the technology innovation team’s innovation capability.