Based on organizational difference perspective, this paper studies the influence of organizational proximity on knowledge transfer and innovation performance of Industry-University-Research collaborative partners. Using a survey of 328 enterprises, the empirical analysis shows that: (1) organizational proximity has a significant role in promoting Industry-University-Research collaborative innovation performance; (2) knowledge transfer plays the mediating role of this relationship as the key mechanism; (3) big data adoption positively moderates the mediation effect, that is, big data technology can effectively realize knowledge transfer among partners and improve innovation performance. This study not only enriches the theoretical and empirical research in the field of Industry-University-Research collaboration, but also provides guidelines for the governments, enterprises, and institutions.