Interdisciplinary cooperation is an important way to achieve scientific innovation breakthrough. Currently, great scientific innovation often occurs in interdisciplinary areas. However, they still face challenges in relation to theoretical support and strategic choices. This paper identifies the extent to which interdisciplinary cooperation-induced heterogeneity affects team innovation performance in Chinese universities. The questionnaire survey is employed in this study and the samples selection covers a wide range of multidisciplinary or interdisciplinary collaboration. This study used Poisson regression analysis to create a new method to evaluate innovation performance. Then, the relationship between team heterogeneity and innovation performance was examined and the moderating role of transformational leadership was also introduced. The empirical results show that three independent variables (disciplinary heterogeneity, cognitive heterogeneity, and organisational heterogeneity) all had a significant positive effect on the team innovation performance. Transformational leadership has a significant positive effect on cognitive heterogeneity and innovation performance, but moderating effects did not appear to be seen in the other two relationships. Our study contributes to a deeper understanding of the value of interdisciplinary research collaboration.