Policy-driven reform for excellence in higher education was implemented in Taiwan in 2005. The effects of the policy implementation vary among campuses. In particular, the limited effects of critical areas in university–industry collaboration have become a public concern. In this study, we assumed that organizational heterogeneity is a key factor influencing the effects of university–industry cooperation policy in higher education institutions. We considered that faculty position, faculty member nationality, and diversity in academic expertise as indicators of heterogeneity according to the concept of Blau’s index. One-hundred graduate institutions with doctoral programs were selected from 881 departments offering doctoral programs in Taiwan as our target group. Correlation analysis, regression analysis, and curve estimation were conducted to determine the effects of graduate institution heterogeneity. 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. Heterogeneity in nationality positively influenced university–industry collaboration. Diversity in expertise in graduate institutions also indicated improved performance in university–industry collaboration. To enhance university–industry collaboration, this study first suggests that the optimal fit proportion of faculty numbers in graduate institutions is 7 professors to 2 associate professors to one assistant professor. Second, recruiting more faculty members with different nationalities is an effective approach for enhancing institution performance in university–industry collaboration. Finally, determining how to diversify the expertise in graduate institutions is critical for improving performance and must be considered at specific institution level. The findings reveal some specific strategies for graduate institutions to reallocate their human resources to optimize their performance in this field.