Microelements are vital for regulating organismal growth and maintaining ecosystem structures and functions. Microorganisms help cycle microelements in soil; however, their regulatory mechanisms in dry desert regions remain unclear. To address this research gap, we performed metagenomic sequencing to analyze the rhizospheric microbiological community structures and functional gene profiles of three typical halophyte bushes in the Ebinur Lake Basin under natural drought stress gradients to reveal the response mechanisms of the functional genes of soil microbial microelements on rhizospheric effects and drought stress. As drought stress decreased, sand significantly decreased, whereas silt and soil organic carbon (OM) significantly increased ( P < 0.05). In the key pathways of the microelement cycle, cbiN for Ni and Co transport, znuA for Zn transport, mntBC for Mn) transport, sitABCD for Fe and Mn transport, and nikC for Ni transport showed a significant positive correlation with drought intensity, suggesting enhanced microelement transport under drought conditions. BG and NAG significantly affected the functional genes of soil microelement transport processes in the rhizosphere under mild to moderate drought, whereas silt and clay significantly affected the functional genes of the soil microelement transport process in the rhizosphere under severe drought stress. Proteobacteria and Actinobacteria were the dominant microbial taxa that participated in soil microelement cycling. Overall, the microbial regulation of soil microelement cycling was jointly influenced by drought stress and rhizospheric effects. These findings enhance our understanding of the microelement cycling mechanisms in arid regions and provide new theoretical and scientific support for studying material cycling in desert ecosystems.