The close links between desert biodiversity and ecosystem multifunctionality (EMF) in arid areas have continued to attract attention in the field of eco-sciences. This paper explores the relationship between biological diversity and EMF, as well as the relative contributions of biotic and abiotic factors to EMF along soil water gradients, using field sampling and laboratory measurements in the desert plant communities of the Ebinur Lake Wetland National Nature Reserve (ELWNNR) in Xinjiang. The results showed that the contributions of plant diversity to EMF differed across soil water, with functional diversity playing a dominant role in both soil high (H) and low (L) water, and being primarily driven by phylogenetic diversity in soil medium water (M). Bacteria were more abundant than fungi in desert ecosystems, and soil moisture significantly influenced microbial alpha diversity and community composition, which in turn affected their relationship with EMF. The degree of ecological niche differentiation and resource competition among plants within the community (FDiv) directly influenced EMF levels (standardized direct effect value of -0.423). Plant diversity provided stronger predictions of EMF compared to microbial diversity. Structural equation modeling with biotic and abiotic factors as predictors confirmed the significant direct effects of both on EMF, with the abiotic factor (soil salinity) showing the strongest significant positive direct effect (standardized direct effect value of 0.643), followed by the third axis of the biotic factor (Bio_PC3) (0.390). This study aims to provide new insights and theoretical support for the maintenance and enhancement of EMF in the region.