In the context of modernizing grassroots governance system and governance capacity， micro-governance is an important direction for the transformation of rural governance, which is based on unit subsidence of rural governance and life transition to improve the refinement of rural governance. Therefore，The analysis of the generation logic and operation mechanism of micro-governance is grounded on the perspective of “system and life” theory. On the one hand， micro-governance effectively deals with the institutional environment of villagers’ self-governance sinking， responds to the differentiated living needs of villagers， and timely handles “micro-affairs” in daily life practices. On the other hand， micro-governance takes the villager group as the unit of governance and builds the internal elements of “micro-community”， “micro-grid” and “micro-organization” to promote the reconstruction of rural governance community， the reshaping of governance methods and the integration of governance resources. Micro-governance reconstructs the form and content of rural governance presenting a pluralistic structure of governance subjects， institutionalized governance rules and “carrot-and-stick” governance strategy in governance practice. As a new mode of rural governance in the new era， micro-governance can enhance the subjectivity of villagers， optimize the structure of rural governance， and help modernize the rural governance system and governance capacity.