The eco-environment provides various spaces, conditions, and resources for human development, and their quality is a significant factor affecting sustainable development in a region. Most drylands face environmental fragility due to problems such as infertile land, scarce suitable living space, and a lack of resources. Therefore, investigating the temporal and spatial changes in the eco-environment of drylands is vital to developing them sustainably. This paper takes Hetian, which is located in the Tarim Basin of Western China and has typical features of an arid (or a hyper-arid) region, as the research area. The ecological index (EI) was used to construct a comprehensive ecological evaluation system, and five sub-indices (the biological richness index, vegetation coverage index, water network denseness index, land stress index, and pollution load index) were calculated to identify the quality and changes in the eco-environment of Hetian in 1995, 2009, and 2018. The results show that, from 1995 to 2018, the EI in Hetian showed a continuous downward trend (from 24.76 to 16.32), representing a change (ΔEI) of −8.44; this indicates significant deterioration in the quality of the local eco-environment. Large fluctuations in the EI also suggests that the environment in Hetian is very sensitive. In addition, the results revealed a degradation of Hetian, which includes a hyper-arid region.