Aims Soil biota play a crucial role in maintaining ecosystem functions, particularly in arid environments where belowground biodiversity is essential for soil health and resilience. However, the vertical distribution patterns of soil biota in desert ecosystems dominated by a single plant species, such as Calligonum mongolicum, remain poorly understood. Methods This study employs high-throughput Illumina sequencing to investigate soil microbial and faunal communities across six soil depth profiles (0-100 cm) within a C. mongolicum-dominated desert landscape. Results Results indicate that alpha diversity of fungi, archaea, and metazoa increases with depth, whereas protists show a contrasting trend, and bacterial diversity remains relatively stable. Soil depth significantly influences beta diversity, particularly in archaea, and protists, as demonstrated by non-metric multidimensional scaling (NMDS) analysis. Key microbial and faunal groups identified include Actinomycetia, Sordariomycetes, Nitrososphaeria, Filosa-Sarcomonadea, and Nematoda, with their distribution closely linked to soil physicochemical properties. Available potassium (AK), soil water content (SWC), and available phosphorus (AP) emerge as the primary environmental drivers of biotic community structure. Actinomycetia were significantly influenced by AK, AP, and SWC, while Sordariomycetes correlate with total potassium (TK) and SWC. Nitrososphaeria exhibit a strong association with SWC and AP, Filosa-Sarcomonadea with AK, and Nematoda with SWC. Conclusions These findings highlight the critical interactions between soil biota and edaphic factors in shaping ecosystem dynamics in arid regions. Understanding these patterns is essential for informing sustainable land management strategies, desertification mitigation, and ecosystem restoration efforts in fragile desert environments.