<p>In the context of climate change, dramatic fluctuations in extreme hydrological events pose threats to ecosystem properties, resulting in the destruction of biodiversity and ecosystem functions. Desert–wetland ecosystems are ecologically important in inland river basins in arid zones; however, the mechanisms by which biodiversity affects desert–wetland ecosystem multifunctionality remain unknown, leading to the lack of a necessary theoretical basis for targeted conservation strategies. In this study, we evaluated the ecosystem multifunctionality of the Daliyabuyi Oasis, using averaging and multiple threshold approaches. The relative contributions of community-weighted mean traits, diversity indices, and environmental factors to ecosystem multifunctionality were analyzed. The results showed that the multifunctionality of desert–wetland ecosystems was mainly driven by the mass ratio effect. Community-weighted mean height was recognized as the most critical factor due to its significant positive effect on ecosystem multifunctionality. Surface water disturbance may exert a negative indirect effect on multifunctionality through community height, while groundwater depth could have a positive indirect effect on multifunctionality through three mediating variables: Soil total dissolved solids, phylogenetic diversity, and community height. This study supports the intermediate disturbance hypothesis from the perspective of ecosystem function and clarifies the continuum of multifunctionality among surface water, groundwater-soil, and vegetation-ecosystem interactions. It emphasizes that floodplain habitats can have additional negative impacts on multifunctionality. The results of this study aim to offer scientific insights for conserving ecosystem multifunctionality based on community attributes and to present new perspectives on the evolution of desert-wetland ecosystems in the context of global change.</p>