Arid ecosystems are subject to extreme and persistent environmental stress, yet the mechanisms underlying their structural stability and functional persistence under global change remain poorly understood. Although rigorous study on the geographical distribution patterns of microbial communities and their climate-driven mechanisms under climate change is still lacking, deserts play a critical role in global biogeochemical cycles. This study integrates field-collected samples with publicly available sequencing data, using machine learning based spatial prediction techniques to investigate the environmental regulation mechanisms of microbial community structure and functional characteristics across multiple deserts. By integrating these maps with future climate scenarios, we assess the potential impacts of environmental change and human activities on microbial distribution dynamics. Results indicate that desert microbial ecosystems are primarily shaped by deterministic environmental constraints rather than spatial succession. Aridity index, precipitation, temperature, and vegetation cover exert the strongest influence on desert bacterial species richness and functional diversity. Under the SSP245 scenario, microbial diversity and richness are projected to decline by 2.7%, while phylogenetic diversity is expected to increase by approximately 1.6% by 2030, 2050, and 2100. In contrast, the SSP585 scenario shows diversity and abundance increasing until 2050, followed by a decline by 2100, with Shannon diversity decreasing by 4.3% and phylogenetic diversity fluctuating within +/- 3.6% of current values. This study establishes a comprehensive baseline for the spatial distribution and ecological functions of desert microbial communities, thereby improving predictions of arid ecosystem responses to future climate change and degradation, and highlighting the role of desert microbes in climate feedbacks as well as ecosystem resilience under ongoing global warming and desertification.