The future of the ecologically fragile areas on the Qinghai-Tibet Plateau (QTP) is a matter of concern. With the implementation of the Western Development Strategy, the Lanzhou-Xining Urban Agglomeration (LXUA) has encountered conflicts and compromises between urban expansion, ecological protection, and farmland protection policies in the rapid development of the past 2 decades. These deeply affect the land use layout, making the ecological sustainable development of the ecologically fragile areas of the QTP a complex and urgent issue. Exploring the impact of different policy-led land use patterns on regional ecosystem services is of great significance for the sustainable development of ecologically fragile areas and the formulation of relevant policies. Following the logical main line of “history-present-future”, the Patch-level Land Use Simulation (PLUS) model, which explores potential factors of historical land use, and the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model were used to construct three future scenarios for the modernization stage in 2031 dominated by different land use policies in this study. These scenarios include the Business-as-Usual Scenario (BS), the Cropland Protection Scenario (CP), and the Ecological Protection Scenario (EP). The study analyzed and predicted land use changes in the LXUA from 2001 to 2031 and assessed carbon storage, habitat quality at different time points, and water yield in 2021. The results indicated that land use changes from 2001 to 2021 reflect the impacts and conflicts among the Western Development Strategy, ecological protection policies, and cropland preservation policies. In 2031, construction land continues to increase under all three scenarios, expanding northwards around Lanzhou, consistent with the actual “northward expansion” trend of Lanzhou City. Changes in other land uses are in line with the directions guided by land use policy. By 2031, carbon storage and habitat quality decline under all scenarios, with the highest values observed in the EP scenario, the lowest carbon storage in the BS scenario, and the lowest habitat quality in the CP scenario. Regarding water yield, the LXUA primarily relies on alpine snowmelt, with construction land overlapping high evapotranspiration areas. Based on the assessment of ecosystem services, urban expansion, delineation of ecological red lines, and improvement of cropland quality in the LXUA were proposed. These findings and recommendations can provide a scientific basis for policy makers and planning managers in the future.