Member satisfaction is a crucial metric to measure the development of farmer professional cooperatives. Research on the impacts of organizational fairness on cooperative member satisfaction can provide a decision basis for the standardization of the internal system of cooperatives. Based on a survey data of 490 cooperative members from 6 counties (cities and districts) in Yunnan Province, this paper analyzed the impacts of organizational fairness on cooperative member satisfaction and explored its mechanism and heterogeneity by Oprobit model and intermediary effect model. Results show that only 35.51% of cooperative members are relatively satisfied or very satisfied, indicating significant room for improvement in overall member satisfaction. The proportion of core members satisfied is higher than that of non-core members, and the proportion of model members satisfied is higher than that of non-model members. Organizational fairness plays a significant role in enhancing cooperative member satisfaction. From the perspective of mechanism, organizational fairness promotes cooperative member satisfaction by promoting organizational identity and trust. Further heterogeneity analysis shows that organizational fairness can significantly improve the satisfaction of non-core members, whereas its effect on core members is insignificant. The impact of organizational fairness on the satisfaction of non-model cooperative members is significantly higher than that of model cooperative members. Therefore, to further enhance cooperative member satisfaction, this paper provides the following countermeasures and suggestions: improving the construction of cooperative system, encouraging members to participate in internal affairs, standardizing the development of cooperatives, strengthening communication among members, and enhancing the driving ability of model cooperatives..