The engagement of farmers in the governance of farm irrigation systems is crucial for meeting irrigation demands and enhancing farm productivity. Theoretically, grassroots organizations' concerns and support for farmers will encourage them to participate in the activities of the organization, thus improving the management performance of the irrigation system. This paper examines the influence of organizational aid on the governance of agricultural irrigation systems using field survey data in the Yellow River basin, China. The seemingly unrelated regression model is used to explore the group disparities under distinct organizational circumstances and farm household characteristics. The study demonstrates that the software and hardware support provided by organizations can promote improved management performance of irrigation systems. In addition, considering the heterogeneity of organizational environments, such support is more conducive to enhancing the governance of systems in organizations with more cooperative atmospheres and higher degrees of fairness. From the perspective of the heterogeneity of system users, providing organizational support to growers with a low degree of nonagricultural transformation and labour shortage is more conducive to improving governance performance. Consequently, establishing an excellent organizational atmosphere and targeting organizational support to farmers is a viable means to optimize the governance of irrigation systems.