Rural population has continually declined in response to the rapid urbanization process occurring in China, and the related negative socioeconomic impacts on rural development have attracted considerable attention from scholars. Currently, few studies have investigated the eco-environmental impact of rural population decline. By employing remote-sensing data, including land-use and normalized difference vegetation index (NDVI) data, this study proposed a method based on the eco-environmental quality index (EQI) to measure the changes in the rural eco-environmental quality (REQ) at the prefectural level from 2000 to 2020. Then, we examined the impacts of rural population decline on REQ variations. We found that (1) most of the research units experienced continuous rural population decline during the research period, with the rural population density declining more than 25% from 2010 to 2020 in approximately half of the research units; (2) the REQ improved in most of the units, especially in the western region, but there were still many units that experienced a decline in the REQ, which were primarily concentrated in the coastal and central regions; (3) rural population decline improved the REQ, but its impacts varied regionally; and (4) rural population density, natural factors, and eco-environmental protection programs had significant influences on REQ variations. These findings may provide a reference for sustainable-development policies in rural China and other developing countries.