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This paper discribes the definition of ecosystem health for the water-level flutuation zone of the Three Gorges Region and puts forward an evaluation system involving indicators in three groups: 1) structural indicators comprise slope, biodiversity,environmental capacity, stability, restoration ability and damage situation; 2) functional indicators including probability of geological hazard, erosion rate, habitat rate, land use intension and days of tourist season; 3) environmental indicatiors made up of population quality, potential intension of human, ground water quality, ambient air quality, wastewater treatment rate, pesticide use rate, fertilizer use rate, environmental management and public participation. In the design of the system, the subject zone is regarded as the type similar to wetland and the impacts of human activities on the zone are attached great importance to.