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The long-term impacts of climate change and human activities have resulted in the Yanhe watershed, a typical watershed in the Loess Plateau region, exhibiting a high degree of vulnerability and significant heterogeneity in ecological environmental quality. This has led to environmental degradation and complex socio-ecological challenges. Consequently, there is an urgent need to carry out research on the spatial and temporal differentiation patterns of ecological environment quality. By utilizing remote sensing data spanning 21 years, this study evaluated the evolutionary trends and consistency of ecological environment quality (EEQ) within the Yanhe watershed based on the remote-sensing-based ecological index (RSEI). Furthermore, it examined global and local spatial autocorrelation of the RSEI by constructing a hexagonal grid, thereby revealing the spatiotemporal characteristics of EEQ at different scales within the Yanhe watershed. The results were as follows: (1) The EEQ has exhibited an overall upward trend in the past two decades, while it has displayed significant fluctuations; (2) the Global Moran’s I values for the years 2000, 2010, and 2020 were 0.18, 0.32, and 0.21, respectively, indicating a presence of spatial autocorrelation within the RSEI; (3) the overall EEQ of the Yanhe watershed will continue to improve, although the ecological quality in certain areas remains unstable due to local natural conditions and human activities. This research not only contributes to the technical framework for analyzing the spatiotemporal heterogeneity of EEQ but also provides actionable insights for ecosystem restoration and sustainability within the Loess Plateau watershed. Our work advances the understanding of ecological dynamics in semi-arid regions and offers a model for assessing ecological quality in similar environmental contexts.