Abstract: Three Gorges Reservoir Area is China′s strategic water source for water resources allocation, and the evaluation of its sustainable carrying capacity of water resources is of great significance to the regional realization of high-quality development. This paper proposed the water resources ecological footprint model including water resource footprint and water pollution footprint to study the spatio-temporal evolution of water resources ecological footprint and ecological carrying capacity in Three Gorges Reservoir Area from 2002 to 2016. The results showed that the overall water resources ecological footprint in Three Gorges Reservoir Area performed a fluctuating trend of first rising and then declining from 2002 to 2016, and the utilization efficiency of water resources and water pollution situation have been gradually improved. The ecological carrying capacity of water resources was greatly affected by rainfall. From 2002 to 2016, the ecological carrying capacity of water resources was greater than the ecological footprint, indicating that there was a certain ecological surplus of water resources. That is to say the sustainable utilization of water resources in Three Gorges Reservoir Area was well. The distribution of water resources utilization in Three Gorges Reservoir Area was extremely uneven. The key ecological functional area located in the head area of the reservoir where water resources are less demanded was rich in water resources and had large ecological surplus. On the contrary, the key development area located in the tail region where water resources are highly demanded was short in water resources and had small ecological surplus. Ecological deficit arose in 11 districts of Yuzhong, Yubei etc., showing the utilization of water resources was in an unhealthy state. The changes of water resources ecological footprint were closely related to socio-economic development; and the spatio-temporal distribution of water resources in Three Gorges Reservoir Area should be fully considered. The industrial structure should be adjusted and the water use efficiency should be improved. The water resources should be rationally allocated and utilized, so as to promote the sustainable development of the social and economic environment in the Three Gorges Reservoir Area.