The coupling and coordinated relationship between the ecological environment and carbon emissions is critical to the sustained development of human society. The remote sensing eco-index (RSEI) model has been applied to the assessment and monitoring of ecological environment quality, but RSEI neglects air pollution, and thus this study introduced aerosol optical depth (AOD) into the index system and constructed a novel ARSEI to evaluate the ecological environment quality and analyze the spatial-temporal changes in ARSEI and energy-related carbon emission (ECE) at the county level in China. Additionally, we further investigate the local relationship between ARSEI and ECE in China by using the coupled coordination model (CCD). The outcomes showed that: (1) Compared with the RSEI, the ARSEI widened the gap in ecological quality between the east and the west along the Heihe-Tengchong line; (2) ARSEI value was significantly increased in 24.70% of areas in China, mainly in the Northeast Plain, Loess Plateau, and Tarim Basin. ARSEI value was significantly decreased in 5.35% of areas in China, mainly in the Qinghai-Tibetan Plateau, the northern part of the Tianshan Mountains, eastern coastal cities, and central urban agglomerations; (3) ECE dispersed from east to the west from 2000 to 2017, with an average annual increase of > 0.3 megatons in 354 counties, densely distributed in the eastern coastal urban agglomerations, Loess Plateau, and sporadically distributed in some central and western cities in China; (4) CCD distribution showed a “west-low-east-high” pattern, with an upward trend in CCD value in the majority of surveyed counties (2,241), and a downward trend in some counties (171) in southwest, south, and central China. Based on these results, recommendations are proposed at the county and above levels for coordinated and sustainable development of urban economy and ecology.