Research on changes in cryosphere services is crucial for the responsible management of cryospheric resources and for fostering sustainable development in Social-Ecological Systems (SESs) impacted by the cryosphere. While previous research has primarily focused on quantifying cryospheric change through Cryosphere Service Value (CSV), the impact of cryosphere service change on Social-Ecological Systems Resilience (SESR) remains unclear. This study considers the Qilian Mountains as a cryosphere system and assesses the changes in its service value from 2000 to 2020. It also establishes a framework to analyze the spatial-temporal variations in resilience within the Qilian Mountains Area in China (QMAC) and investigates the impact of changes in cryosphere services on SESR. The findings indicate that (1) the CSV exhibited a decreasing trend followed by an increase from 2000 to 2020, with minor increases observed in the three northern inland river basins and substantial increases in other areas; (2) the resilience in QMAC improved consistently, establishing a spatial pattern characterized by higher resilience in the west and lower resilience in the east, as well as higher resilience in the north and lower resilience in the south; (3) the effects of changes in cryosphere services on SESR demonstrate significant spatial-temporal patterns, the decline in climate regulation service has a notably negative impact on ecological resilience, while the increase in value from aesthetic appreciation and tourism service positively boosts economic resilience; and (4) changes in cryosphere services affect social resilience by influencing residents’ livelihoods, with more pronounced effects on SESs in areas with high land use intensity. This research provides a research avenue for examining how cryosphere service change impacts SESR and offers practical experience for promoting the stability of SESs and developing sustainable development policies in regions affected by the global high-mountain cryosphere amid climate change.