It is a national strategic consideration of planning for entire project of ecological environmental protection and building of reservoir area of the Three Gorges to construct the ecological protective screen of the upper reaches of Yangtze River. Standing on the environment priority, establishing the thinking of rural-urban environment protection integration, making an effort to promote the institutional improvement on ecological environmental protection of reservoir area of the Three Gorges, among these, the inflexion is to form a new administrative thought pattern, the basic point is to construct a three levels of comprehensive management system: the node is to establish a new governmental action pattern and promote the recycling economic development mode of reservoir area of the Three Gorges, the emphasis is to perfect the operational mechanism of rural-urban coordinated ecological environmental protection, reform the pollution charge and implement the institution of pollution discharge standards and total volume control quotas for pollutants while accelerateing the economic development of reservoir area of the Three Gorges and practically protecting ecological environment, establishing urban-rural integrated ecological protective screen and realizing the rural-urban ecological building and environmental protection coordinated development. Based on deep survey on ecological environment reservoir area of the Three Gorges of Chongqing, this article emphatically points out the countermeasures and suggestions on structural mode and operational system of integrated ecological environmental protection of reservoir area of the Three Gorges.