Common prosperity is the core goal of rural revitalization, and the sustainable growth of farmers’ income is an inevitable requirement. This study uses CLDS2014-2018 village- and family-level questionnaire data to reveal how the degree of village organization affects the sustainable growth of farmers’ income, thus providing a reference for local government decision-making to promote the increase in farmers’ income and narrow the income gap at the village level. The results show that the degree of village organization can significantly affect farmers’ income, and the analysis results of the degree of formal organization are consistent with this. Specifically, for every 1% increase in the degree of village organization, the per capita household income will increase by 0.324%, among which, the wage income will increase by 0.226%, the operational income will increase by 5%, the property income will increase by 0.008%, and the transfer income will increase by 0.042%. The estimation results obtained by using instrumental variables are consistent, and the results are robust. At the same time, improving the degree of village organization can also significantly increase the proportion of farmers’ non-agricultural income and narrow the income gap among farmers. On the impact of heterogeneity, it was found that the geographical distance between villages and county and township governments, as well as the political identity and education level of farmers, will affect the role of the degree of organization. The results of the mechanism analysis show that improving the degree of village organization is mainly achieved by promoting the circulation of agricultural land, socializing the service of agricultural machinery, and providing industrial and commercial capital to the countryside to increase farmers’ income. The research revealed that the modernization of rural governance should be accelerated and the degree of village organization should be improved, especially the degree of formal organization, so as to build benign trust and a cooperative relationship between village committees and villagers and implement policies and measures that improve the income of farmers according to local conditions. At the same time, this will strengthen the publicity and education of party members to improve the proportion of rural party members and the education level of farmers.