Abstract: Exploring the trade-offs and synergies between regional ecosystem services and the allocation of environmental resources is critically important for guiding the management of ecological environment. Data on land use, meteorological observations, and soil and socio-economic statistics were collected in 2000, 2010, and 2018 to characterize spatio-temporal changes in four types of ecosystem services, including water conservation, soil conservation, carbon sequestration, and biodiversity maintenance in the Three Gorges Reservoir Area. The trade-offs and synergies between ecosystem services were analyzed at two spatial scales: the global scale and comprehensive zoning based on hot spots. The results show that: (1) From 2000 to 2018, water conservation and soil conservation services in the Three Gorges Reservoir Area first decreased and then increased, and there was a significant change in their spatial pattern. Carbon fixation increased annually, with a total increase of 11.45% from 2000 to 2018. The spatial pattern of biodiversity remained unchanged, but there was a small decrease in 2018; thus, the risk of ecological degradation requires increased attention. (2) In the Three Gorges Reservoir Area, the proportion of non-hot spot areas, type 2 hot spot areas, and type 4 hot spot areas first increased and then decreased; the proportion of type 1 hot areas and type 3 hot areas first decreased and then increased. (3) There was synergy between all types of ecosystem services in the Three Gorges Reservoir Area at the global scale, and the correlation coefficients of ecosystem services between different hot spots and global scale were significantly different because of variation in regional land-use types and natural resources.