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• Bacteria and eukaryota diversity increased with increasing longitude and elevation. • Archaeal diversity decreased slightly with increasing elevation. • Some phyla diversity patterns are individually inconsistent with the overall trend. • Geographic distance contributed more than environmental factors to soil microbes. • More intra-domain than inter-domain links within the soil microbial network. Recent studies show that different microorganisms, especially bacteria and fungi, exhibit contrasting latitudinal, longitudinal, and altitudinal diversity patterns at a global scale, but little is known about biogeographic patterns in desert ecosystems. In this study, we chose a narrow geographic channel, namely the deserts of northern China's Hexi Corridor as the study area. Based on field survey and next-generation sequencing (Illumina MiSeq PE300 Platform), to map soil microbial geographic diversity patterns in this area and further determine the main driving factors responsible for shaping the soil microbial community. The results show that bacteria and eukaryotic diversity increased linearly with increasing longitude and altitude, but decreased with increasing latitude in the Hexi Corridor deserts, whereas archaeal diversity showed little change along these geographic gradients. Some individual phyla within the bacterial, archaeal, and eukaryota communities were not always consistent with collective trends, e.g., for the α-diversity of the ten most dominant bacterial phyla, only six phyla showed a statistically significant increase with altitude. The soil microbial community composition was jointly shaped by geographic distance and environmental variables (regional climatic factors and local edaphic variables). The effect of geographic distance on the soil microbial community composition was slightly stronger than that of the environmental variables. Intra-domain links were stronger than inter-domain links in the soil microbial network of the Hexi Corridor deserts, and these links were mostly positive. Although bacteria formed more connections than both archaea and eukaryotes, removing the archaea resulted in a lower natural connectivity, suggesting that the archaea were the core group for building this desert region's soil microbial co-occurrence network. Taken together, these findings deepen our understanding of regional-scale soil microbial diversity patterns in this desert ecosystem. [ABSTRACT FROM AUTHOR]