As the most important ecological barrier and ecological corridor in Southwestern China, the Three Gorges Reservoir region was strategically important and significant. Since the 1990s, in company with the accomplishment of the Three Gorges hydro-junction project, a series of key national ecological and forestry projects have been initiated, including the protective forests along the Yangtze River, the natural forests and Resources conservation, the conversion of cropland to forest, the afforestation of the reservoir surrounding area and the afforestation of both banks of the Yangtze River. These have led to significant changes of land use and land cover (LULC) types and their spatial distribution. More than twenty years has been gone. However, it is unknown that how the accomplishment of the ecological projects affected the change of ecosystem service values and what were the effects of these projects on the protection of the Three Gorges Reservoir region. There is a strong need to assess the effectiveness of the projects, including the dynamics of LULC types and the induced changes of ecological service values. The objective of this study was to analyze the spatiotemporal characteristics of ecological service changes and investigate the factors that have driven the dynamics in the Three Gorges Reservoir region. In this study, the Landsat Thematic Mapper^TM images that cover the Three Gorges Reservoir region were acquired for years of 1990, 1998, 2006 and 2011, respectively, and visually interpreted for LULC types. The per unit ecosystem service equivalent value of the ecosystems within the region was calculated by using the corresponding value of the terrestrial ecosystems for the whole country as a reference and the ratio of the per unit grain productivity of the study area to the corresponding value of the country as a revised coefficient. The obtained per unit ecosystem service equivalent value was further modified based on the value of biomass from forested land related to ecological service value. The changes of ecological service values induced by LULC dynamics and corresponding driving factors were quantitatively analyzed by combining land use structure index and ecological sensitivity index. The results showed that (1) during the past twenty one years, the ecological service values of the Three Gorges Reservoir region were mainly supported by the forested land with a percentage of 76.75%, followed by the water and cropland land (23.19%), and the contribution of the grassland was the least (0.22%). The total ecological service value increased from 47.96 billion yuan in 1990 to 68.08 billion yuan in 2011; (2) All the ecological service values increased except food production. The value from soil formation and protection had the greatest increase with an increment of 3.66 billion yuan, followed by the gas regulation (3.31 billion yuan); (3) The analysis of driving factors showed that the changes of the ecological service values were mainly due to human activities, especially the great change of the area for each of the natural ecosystems since the conversion of cropland to forest started in 1998. Moreover, the effects of both the health of the nature ecological systems and the social policy on the changes of the ecological service values could not be ignored. The findings implied that enhancing the protection of LULC types that have higher ecosystem service values, including forested land, grassland, water bodies and so on, is an effective way to stabilize the ecosystems of the Three Gorges Reservoir region.