Environmental footprint represents the degree of the impact of human development on the environment. Environmental footprint and human well-being are the important indicators to measure the sustainable development capacity of a region. This paper calculated the environmental footprint and environmental boundary of the Three-River Headwaters region, constructed a framework for evaluating human well-being in the Three-River Headwaters region, and evaluated the coupling coordination relationship and the dynamic characteristics of the environmental footprint and human well-being in the Three-River Headwaters region from 2000 to 2018. The quantitative relationship between the environmental footprint and human well-being in the Three-River Headwaters region was obtained. The results indicated that:(1) overall, the environmental footprint per capita of the Three River Headwaters region from 2000 to 2018 exceeded the environmental boundary limit. (2) Human well-being in the Three River Headwaters region indicated that social and cultural well-being was higher than safety, health, and basic needs in the order of importance. From 2000 to 2018, the overall human well-being in the Three-River Headwaters region showed a fluctuating upward trend, of which safety and health fluctuated the most and contributed the most to the overall human well-being. (3) The coupling degree and coupling coordination degree between the environmental footprint and human well-being in the Three River Headwaters region showed a fluctuating upward trend, and the level of correlation between the two gradually increased, and gradually tended to be coordinated. The results of this study can provide scientific support for the relevant departments to formulate reasonable regional development strategies.