[Objective] To reveal the spatial-temporal changes of the ecosystem services in the key ecological functional reservoir of the Three Gorges area in Chongqing from 2000 to 2010, in order to provide basis for the sustainable management of ecological environment in the Three Gorges area. [Methods] Based on RS and GIS techniques, four major ecosystem services including biodiversity maintenance, soil conservation, water conversation and carbon fixation were used to establish the evaluation models. [Results] (1) During the decade, the high level area of the functional ecosystem services in the research area increased by 386.14 km². (2) For each single ecosystem service function, the high level of the water conservation increased by 4 016.4 km²; the high, relatively high and medium level of the soil conservation increased by 516.2 km², 2 825.9 km² and 2 493.8 km² respectively. (3) From the spatial distribution, the better functional areas of the ecosystem services were mostly distributed in the north of Kaixian County, the north of Wushan County, the South of Fengjie County, and both sides of the tributaries of the Yangtze River and the region of the strap shaped ridge covered with better vegetation. The poorer functional regions of the ecosystem services were mostly distributed in Changshou County, Dianjiang County, the flat terrain areas of Liangping, steep terrain and ecological disaster-prone areas of Kaixian, Yunyang, Fengjie, Wushan Counties. [Conclusion] During the decade, the biodiversity maintenance function and the water conservation trend to rise; the soil conservation and the carbon fixation function are generally poor, but both are on the rise trend; the area of improvement is distributed in the new wetlands on both sides of the trunk stream of the Yangtze River formed by seasonal water inundation.