The Qilian Mountain is a crucial water conservation area and ecological security barrier in arid regions of northwestern China. Recently, regional ecological stability and restoration capacity face significant challenges, Ecosystem health and restoration benefits urgently need to be evaluated for regional ecological management and sustainable development. Based on multi-sources data and various numerical simulation methods, an assessment framework that covered three dimensions (ecosystem structure, quality, and services) was established to analyze the spatio-temporal patterns of ecological restoration benefits in the Qilian Mountains during 2000-2020, and the dominant driving factors was identified by using the Random Forest model. The results showed that: (1) From 2000 to 2020, ecosystem structure, quality, and services in the Qilian Mountains continuously improved. Spatially, water conservation, soil retention, and carbon storage services were higher in the east and lower in the west, while sand fixation services showed the opposite pattern. (2) The comprehensive benefits of ecological restoration remained relatively low (0.23). During 2000-2020, areas with improved benefits accounted for 52.62%, including 21.30% with precipitation and vegetation, were the dominant drivers of ecological restoration benefits, with an explanatory power exceeding 93.74%, while socioeconomic factors contributed less than 6.26%.