Desert ecosystems, particularly in arid regions like the Tengger Desert, are highly sensitive to both anthropogenic activities and climate change, making the monitoring and evaluation of ecological quality critical for sustainable management and restoration efforts. This study analyses the spatiotemporal evolution of ecological quality in the Tengger Desert from 2001 to 2021 using the Remote Sensing Ecological Index (RSEI), incorporating meteorological factors (temperature, precipitation, wind speed), topographical factors (elevation, slope, relief) and anthropogenic indices (land use and land cover). The mean RSEI fluctuated between 0.1542 and 0.2906, indicating poor ecological quality, with a peak in 2008 attributed to national ecological projects. Despite initial improvements, overall ecological quality declined at a rate of 0.0008 a−1 from 2008 to 2021. Spatially, degradation was most pronounced in the central and southern areas. Due to sand-binding engineering in the Tengger Desert in 2008 and the mountain climate suitable for vegetation growth, improvements occurred in the northeast and southwest. Moran’s I and Hurst index analyses revealed significant spatial clustering of ecological quality and persistence of degradation trends, with over 49.53% of the area projected to experience further deterioration. Geodetector analysis identified land use and land use cover as the most influential factors on RSEI, especially in combination with wind speed, temperature, and precipitation, underscoring the role of both human activities and climate. The study highlights the need for sustained ecological management, particularly in areas showing continuous degradation, to prevent further ecological deterioration.