Xinjiang is an arid and semi-arid region where ecosystems are fragile, and monitoring how its ecology changes over time is critical for its sustainable development. In this study, a Remote Sensing Ecological Index (RSEI) was established for Xinjiang from 2000 to 2025. To understand temporal and spatial changes in ecological quality, we conducted spatial autocorrelation analysis, Theil–Sen median trend analysis, a Mann–Kendall trend test, and Hurst exponent analysis. We also used Geodetector to determine which factors affect the RSEI. The main results were as follows: (1) The RSEI in Xinjiang remained low, with a mean value between 0.285 and 0.336. Mountainous areas had higher values, basins had lower values, and spatial clustering was strong (Moran’s I index: 0.81–0.86). (2) H-H clusters expanded and then shrank, while L-L clusters grew after 2015. Areas with excellent ecological grades increased, but so did areas with poor grades, indicating that improvement and degradation both exist. (3) Most areas were stable, but 19.13% showed persistent degradation, indicating that these areas need more attention. (4) Land surface temperature (q = 0.624) and land cover (q = 0.576) were the main driving factors, and factor interactions showed enhanced effects. The results of this study could provide a scientific basis for ecosystem protection and restoration in Xinjiang.