Based on equity theory and social exchange theory, this study employs empirical research methods to investigate the impact mechanisms of collaboration incentives in intelligent manufacturing enterprise alliances on operational performance, and further discusses the moderating effects of organizational justice in these relationships. The results indicate that both benefit distribution incentives and information sharing incentives significantly positively affect operational performance. Procedural justice significantly enhances the positive impact of information sharing incentives on operational performance, yet it inhibits the facilitative effect of benefit distribution incentives on operational performance. Moreover, the facilitative effect of benefit distribution incentives on operational performance is positively moderated by interactional justice, while distributive justice shows no moderating effect on the relationship between collaboration incentives and operational performance. This paper enriches the research on the governance mechanisms of intelligent manufacturing enterprise alliances and proposes a collaboration incentive model from the perspective of organizational justice, which could help enhance the overall operational performance of the alliances.