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• The impact of precipitation, slope, and swamp wetland ratio on water yield is not affected by spatial scale and watershed. • Identifying key areas for ecosystem services combined with multiple scenarios can help to take ecological restoration. • The water yield in the Baihe basin is more sensitive on climate change, while the water yield in the Heihe basin is more easily affected by land use changes. • The economic development and ecosystem services can both be ensured by wetland ecological restoration. Water supply is one of the core ecosystem services functions for wetland. Due to the important status of Zoige wetland, assessment of water supply in Zoige wetland is significant for ecological security all over the world. In this paper, Heihe and Baihe basins in Zoige wetland were taken as research objects, the water yield module of the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model was used to spatially quantify water supply, with the aims of revealing the driving mechanism of water supply under different basins and spatial scale. We observed the spatial pattern change of water yield under baseline and eleven future scenarios and used the ANOVA of repeated measures and multiple linear regression model to explore the patterns and driving factors of water supply in Heihe and Baihe rivers basins. The research results were as follow. (1) The precipitation is main factor to improve water yield, but this intensity is different in different basins and spatial scale. Topography, climate, vegetation, and percentage of wetland conditions have important impacts on water yield services. However, the impacts of these conditions on water yield were various significantly across different watersheds and spatial scales (excluding factors such as precipitation, slope, and percentage of swamp wetland). (2) The spatial pattern of water yield main was affected by land use change and the amount of water yield main was affected by future climate change. (3) Water yield in the Baihe basin was more sensitive to climate change, while the Heihe basin is more sensitive to land use changes. Wetland ecological restoration strategies can effectively improve regional water yield, especially in the Heihe basin. (4) In all scenarios, the southeast regions of the study region were both the main hot spots of water yield. Wetland ecological restoration strategies have added hot spots in the north regions of the Baihe river basin, reduced hot spots in the middle-south regions of the Heihe basin. [ABSTRACT FROM AUTHOR]