Current research on territorial behavior mainly focuses on the individual level, but both theory and practice have proved the need to further explore the necessity of territorial behavior from the team level. Therefore, this study focuses on the concept of team territorial behavior, based on the theory of harmonious management, and takes 130 research teams from 38 new engineering universities in China as the objects, and reveals the influence of team territorial behavior in enhancing the innovation efficiency of the teams through the mixed methods of empirical sampling experiments, configuration analysis, and case discussion. The results show that: (1) in the context of general theory, team territorial behavior will inhibit the enhancement of team innovation efficiency; (2) in the context of team dependence, team territorial behavior will prompt individuals to form compromised team harmony or involutional team harmony, thus weakening the inhibitory effect of team territorial behavior on team innovation efficiency. Based on the results of this study, we propose two solutions to inhibit team territorial behavior based on “compromised team harmony” and “involutional team harmony”, and suggest that organizations can further strengthen the collective construction of the team and create the special advantages of the platform. It is also suggested that organizations can further constrain the influence boundary of team territorial behavior and enhance the individual’s willingness to work for the organization, so as to achieve the sustainable improvement of team innovation efficiency.