There is a knowledge gap and practical demand to understand the co-evolutionary relationship between rural household livelihood and regional ecological footprints for developing sustainable livelihoods in ecological conservation regions. This paper tracks the change trajectories of rural household livelihoods and regional ecological footprints in four water source areas of the South-to-North Water Diversion Project where various ecological and environmental protection projects and measures are being proposed to protect water quality. As a result, some concerns regarding rural livelihood have arisen. The sustainable livelihood approach developed by DFID (Department for International Development in UK) was used to measure the natural, physical, financial, human, and social capitals of rural livelihoods, while the ecological footprint accounting approach was used to calculate the amount of bio-productive spaces that produce the yearly resource flows for human consumption. The study period is 2000–2014 and data was obtained from the Statistical Yearbooks. The results show that the change trend of natural capitals of rural households, which have increased by 72.5% (SY), 98.8% (NY), 69.3% (TA), and 120.3% (JN) within 15 years, determine the overall change track of rural livelihoods and that rural household livelihood grows with the expansion of regional ecological footprints. Sensitivity of regional eco-footprints to rural livelihood varies from 5.8 to 0.5 in case areas. It is recommended that in the “post South-to-North Water Diversion era”, four policy instruments—population transfer and relocation, industrial restructuring and updating, rural infrastructure and community reconstruction, and cross-ecological compensation—should be adopted to improve sustainable livelihoods in these four water source areas.
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