Land use change is an extremely important factor in ecosystem services and ecological health. A series of problems caused by rapid urbanization and land use changes, such as biodiversity sharp decline, environmental pollution and ecological land loss, continue to affect ecosystem health. The spatially quantitative researches of ecosystem service supply and ecological risk are contributed to scientific management of the regional ecological land, and promote the construction of ecological civilization. In this work, geographic information system (GIS) technology, the accounting model of ecosystem service value, and ecological risk index model, were used to study the spatio-temporal evolution characteristics of ecosystem service supply value and ecological risk index in the Three Gorges Reservoir area (TGR) from 2000 to 2015. Further, the Z-score standardization method is used to construct the ecological function zoning. The research results of the paper are as follows:(1) for 2000-2015 period, the whole change of ecosystem service supply value in the Three Gorges Reservoir area was insignificant. In addition, the ecosystem service mainly played role as regulation service, especially forest land. The ecosystem service supply value in the Three Gorges Reservoir area are highly heterogeneous. High-value supply regions mainly distributed in Yiling District, Zigui County and Xingshan County with high vegetation coverage. Low-value supply regions mainly distributed in Yuzhong District, Yubei District and Shapingba District with high population density. (2) The ecological risk value of the Three Gorges Reservoir area showed a slight upward trend, with a distribution characteristics of "high in the west and low in the east". Ecological safety of the Three Gorges reservoir is gradually transferred to medium risk types. The small and smaller ecological risk areas accounted for more than 55% of the total area. High-risk zone is mainly concentrated in the main city of Chongqing Yuzhong District, Yubei District, Shapingba District and Nanan District, etc. (3) During the study period, the four ecological zones changed little, indicating that the ecological zones kept a relatively stable balance. The distribution continuity of high-supply and high-risk areas (I) is the worst, while the distributions of low-supply and high-risk areas (II) and high-supply and low-risk areas (IV) are more clustered. Based on the study on ecosystem service supply, ecological risks and ecological zoning of the Three Gorges Reservoir area, it contributes greatly to boost the intensive and economical utilization, protects ecological land, and balances economic construction and environmental protection in the Three Gorges Reservoir area.