The innovation of rural governance in the eastern region leads the exploration process of the modern mode of rural governance. Based on the differences of governance content and available governance resources between the eastern rural areas and the central and western rural areas, this paper reveals the different paths of rural governance innovation. The eastern countryside is faced with transactional, mixed and fluid governance content, and formed a governance innovation path with governance units moving up under the support of rich governance resources, while the central and western rural governance mainly faces problems such as agricultural production, project landing and life governance, and formed a governance innovation path with governance units moving down by activating the social mobilization mode. Although there are differences in the logic of governance innovation between the eastern and the central and western villages, they reflect the adaptation of governance objectives and governance means, and effectively respond to their respective governance problems. Therefore, it is necessary to be alert to the possible negative impact of the diffusion of rural governance innovation in the eastern region on rural governance practices in the central and western regions, attach importance to and stimulate the subjectivity of rural governance innovation in the central and western regions, and form a multiple path for the exploration of rural governance modernization.