Abstract: The construction of ecological civilization is a strategic goal for our country to coordinate economic and social development, and a key measure to promote sustainable development. Under the influence of the practice of ecological civilization construction, governance structure in our country has undergone a comprehensive transformation. The overall transformation of county governance structure includes goal transformation, transaction transformation, relationship transformation and governance limit. The overall goal of county governance has changed from pursuing economic GDP to pursuing green GDP; the type of county governance affairs has changed from specialized affairs to overall affairs; departmental relationship of county governance bodies in China has changed from separation to mutual trust, the relationship between government and enterprise has changed from collusion to cooperation, and the relationship between government and society has changed from suspension to embeddedness. However, due to the systematic and long-term characteristics of ecological civilization construction, it is not a temporary task that can be completed at a time. Financial constraints, high standards and corporate bottlenecks constitute the limits of county governance. Therefore, in the specific practice of ecological civilization construction, focus must be on the county-level government's task-taking pressure and regional development pressure, and give local governments a certain buffer space and transition zone.