Abstract: While injecting a lot of resources into the countryside, the project has greatly affected the grassroots ecological governance. Through the study of the operation effects of different projects in the natural villages in Jiangxi Province, we find that the interaction between village autonomy and project operation mechanism in the process of project operation produces different forms of external resources suspension, internalization, externalization, privatization and instrumentalization. Under the background that massive resources continue to be imported into the countryside, it is necessary to select the appropriate operation mechanism with full consideration of the village’s ability to respond. On the basis of improving the level of village public service, we should promote the reconstruction of village’s publicity and improve grassroots governance.