Inner Mongolia is located in China’s arid and semi-arid regions, with sensitive and fragile ecosystems at risk of increased desertification, necessitating ecological restoration. However, economic resources for large-scale ecological restoration are often scarce, so it is vital to identify key areas for ecological restoration. Previous desertification research has focused mainly on the condition and changes in soil or vegetation. However, not all changes in soil or vegetation directly impact humans. New perspectives are increasingly needed to bridge the gap between biophysical and human well-being. We construct a framework to identify priority restoration areas based on ecosystem services and ecosystem vulnerability over a long time series. The results show that: (1) soil conservation services in northeast and southwest Inner Mongolia have degraded. Sand fixation services in central and eastern Inner Mongolia have shown a degradation trend. Habitat quality has been generally stable and sporadic in the past 20 years. (2) The areas with higher ecosystem vulnerability are concentrated in the northeast, mainly due to higher climate exposure and climate sensitivity but relatively lower climate resilience in the northeast. (3) Compared with the results of ecological restoration areas identified based on the trends of traditional vegetation indicators (fractional vegetation cover and net primary productivity), we found a greater proportion of land in northeastern Inner Mongolia in need of restoration. Additionally, there was identified a decreased restoration proportion in southwestern Inner Mongolia to ensure the self-restoration and regulation of desert ecosystems, which is conducive to realizing nature-based solutions.