In capable person governing agricultural cooperatives, the internal governance is essential for cooperatives to achieve sustainable development. As an important mechanism of cooperative internal governance, relational governance is the focus of the current research in the field of cooperative internal governance. Based on the theory of organizational justice, relational embeddedness theory, and relational governance theory, this paper constructs the relationship between interactive justice, relational embeddedness, and governance performance based on fuzzy cognitive map and discusses the influence mechanism of interactive justice on relational governance performance. Taking 245 members of 18 agricultural cooperatives as samples, this paper makes an empirical test by using the machine learning method. Through the analysis of the data, we find that interactive justice has a significant positive impact on the governance performance. Relational embeddedness also has a significant positive impact on the governance performance. And relational embeddedness plays an intermediary role in the positive impact of interactive justice on governance performance. To some extent, the research results broaden the relationship between interactive justice and relational governance performance and provide useful reference for cooperatives to strengthen internal governance and achieve sustainable growth.