<p><i>Agriophyllum squarrosum</i> (L.) Moq., a pioneer species in desert ecosystems, is renowned for its remarkable capabilities in wind erosion control and adaptation to extreme environmental conditions. While plant-associated microbiota plays pivotal roles in host development and resilience to abiotic stress, the composition and ecological functions of endophytic microbial communities in <i>A. squarrosum</i> remain largely unexplored. In this study, we employed high-throughput sequencing of 16&#xa0;S rRNA and internal transcribed spacer 1 (ITS1) regions, combined with functional prediction analyses, to comprehensively characterize the spatial differentiation of endophytic microbial communities across root, shoot, and leaf tissues, and to infer their potential ecological roles in host–environment interactions. Our findings revealed tissue-specific patterns in microbial community assembly, with the highest bacterial diversity observed in roots, and relatively greater fungal diversity in shoots and leaves. Taxonomically, Proteobacteria and Ascomycota emerged as the dominant bacterial and fungal phyla, respectively, with each tissue harboring distinct endophytic taxa of varying abundance. Notably, microbial communities in shoots and leaves exhibited higher compositional similarity. Co-occurrence network analyses demonstrated predominantly positive interactions among endophytic taxa, with root-associated networks displaying greater complexity and robustness. Functional predictions suggested that microbial processes such as nitrogen cycling, carbon assimilation, and cryptic oxygen metabolism—as well as pathways like ABC transporters and two-component systems—may contribute to the adaptive capacity of <i>A. squarrosum</i> in arid desert environments. Collectively, our study elucidates the spatial heterogeneity and ecological potential of endophytic microbial communities across different plant tissues, offering new insights into the microbial mechanisms underlying drought adaptation in desert pioneer plants.</p>