The ecosystems within the Qilian Mountain National Nature Reserve (QMNNR) and its surrounding areas have been significantly affected by changes in climate and land use, which have, in turn, constrained the region’s socio-economic development. This study investigates the regional characteristics and application requirements of the ecological environment in the arid and semi-arid zones of the reserve. In view of the saturated characteristics of NDVI in the reserve and the high-altitude saline-alkali environmental conditions, this study proposed a Modified Remote Sensing Ecology Index (MRSEI) by introducing the kernel NDVI and comprehensive salinity index (CSI). This approach enhances the applicability of the remote sensing ecological index. The temporal and spatial dynamics of ecological and environmental quality within the QMNNR from 2000 to 2022 were quantitatively assessed using the MRSEI. The effect of land use on ecological quality was quantified by analyzing the MRSEI contribution rate. The findings in this paper indicate that (1) in arid and semi-arid regions, the MRSEI provides a more precise representation of surface ecological environmental quality compared to the remote sensing ecological index (RSEI). The high correlation (R2 = 0.908) and significant difference between MRSEI and RSEI demonstrate that MRSEI enhances the accuracy of evaluating ecological environmental quality. The impact of land use on ecological quality was quantitatively assessed by analyzing the contribution rate of the MRSEI. (2) The ecological quality of the QMNNR exhibited an upward trend from 2000 to 2022, with an increase rate of 1.3 × 10−3 y−1. The area characterized by improved ecological and environmental quality constitutes approximately 53.68% of the total area. Conversely, the ecological quality of the degraded areas accounts for roughly 28.77%. (3) Among the various land use types, the improvement in ecological environmental quality within the reserve is primarily attributed to the expansion of forest and grassland areas, along with a reduction in unused land. Forest and grassland types account for over 90% of the total area classified with “good” and “excellent” ecological grades, whereas unused land types represent more than 44% of the total area classified with “poor” ecological grades. Overall, this study provides a valuable framework for analyzing ecological and environmental changes in arid and semi-arid regions.