Abstract: Effective rural governance needs the organic integration of autonomy, rule of law and rule of virtue, and the “three governance” integration is the key to shaping a good rural political ecology. At present, the pain point breakthrough of rural governance needs to clarify the boundary elastic space of autonomy, rule of law and rule of virtue, and promote the innovation of rural governance to operate within the scope allowed by the humanistic boundary, institutional boundary and emotional boundary. Based on the case study of “three governance” integration in Dapu Village, Jinjiang City, Fujian Province, this paper analyzed the effective mode of using boundary flexibility to promote rural governance. The research found that, the mechanism innovation of “three governance” integration lies in establishing an innovation boundary mechanism from the perspective of holistic governance, optimizing the rural political ecology, continuously promoting the path of deep integration, and promoting high-quality “three governance” integration to lead the modernization of rural governance.