Scenario analysis of ecosystem services (ES) can provide a scientific basis for ecosystem management. The objective of this study was to reveal the effects of future land use scenarios on ES in a mountain-oasis-desert system (MODS). We first simulated land use changes for the period of 2015-2035 in Altay Prefecture under three different scenarios: business as usual (BAU), economic development (ED), and ecological conservation (EC). We then evaluated water yield (WY), crop production (CP), soil conservation (SC), sand fixation (SF), carbon sequestration (CS), and aesthetic value (AV) and investigated the multiple interactions among ES at the regional and grid scales. The results showed that SC, CS, and AV continually increased, WY continually decreased under the three scenarios. Our study revealed that the multiple interactions among ES were spatially heterogeneous in the MODS and the spatial heterogeneities changed across scenarios. The locations of and causes for the formation of the multiple interactions among ES were identified based on spatial analysis. This information can help decision-makers develop targeted and differentiated ecosystem management strategies. This study can increase the understanding of the multiple interactions among ES. Our findings can provide a reference for studies of other regions with the MODS structure.