In this study, we assumed that organizational heterogeneity is a key factor influencing the effects of university–industry cooperation policy in higher education institutes. Gender difference, faculty position, faculty member nationality, and diversity in academic expertise were considered as the indicators of heterogeneity. One-hundred graduate institutes with doctoral programs were selected from 881 departments offering doctoral programs in Taiwan as our target group. Correlation analysis, regression analysis, and curve estimation according to the concept of Blau’s index were conducted to determine the effects of graduate institute heterogeneity. Gender difference in graduate institutes played a crucial role on the effect of university–industry collaboration. The results reveal that excessive or insufficient differentiation among faculty positions has an adverse effect on university–industry collaboration, presenting both advantages and disadvantages in this case. A Blau’s index value of 0.56 for faculty position differentiation indicated optimal performance in university–industry collaboration. To enhance university–industry collaboration, this study suggests that the optimal fit proportion of faculty numbers in graduate institutes is seven professors to two associate professors to one assistant professor. Diversity in expertise in graduate institutes also indicated improved performance in university–industry collaboration. Determining how to diversify the expertise in graduate institutes is critical for improving performance and must be considered at specific institute level. The findings provide specific strategies for graduate institutes to reallocate their human resources to optimize their performance in this field.