Ecological governance projects have great potential benefits, but there is a lack of quantitative evaluation of their impacts in terms of enhancing regional ecological carrying capacity under climate change. To quantitatively evaluate the impact of ecological governance projects on regional ecological carrying capacity, a quantitative evaluation model was developed by coupling the classical ecological footprint and ecological service value theory. This model was validated using the water source treatment project (hereinafter referred to as the “DZ” project) of the Middle Route of China’s South to North Water Diversion Project, which is the world’s largest water diversion project, as an example. The results showed the following: (1) During the implementation of the “DZ” project, the per capita ecological carrying capacity of the reservoir area experienced a wave-like growth trend, with an increase of 0.103615 hm2 and a yield increase rate of 20.00%. The “DZ” project has outstanding ecological benefits, valued at approximately USD 125.272266 million. (2) The “DZ” project has contributed to the improvement of the ecological carrying capacity in the Henan area of the Danjiang Reservoir by about 10.14%, demonstrating that such projects have a considerable impact on efforts to improve regional ecological carrying capacity under climate change.