Soil health plays important roles in maintaining food production, plant, animal and human health, and is the foundation of sustainable agricultural development. Soil microorganisms are extremely complex and diverse, including archaea, bacteria, fungi, protists, and virus. They participate in a variety of ecosystem functions and services, such as primary production, nutrient cycling, decomposition, climate regulation and pathogen control, which are closely linked to global food supply and soil health. Arid regions account for about 41% of the world's land surface and sustain more than 38% of the world's population. As an important grain production reserve area in China, the arid and semi-arid region of Northwest China still lacks research on soil health, due to the complexity, fragility and sensitivity of soil ecosystems in this region. In this review, we summarize the relationship between soil microorganisms and the ecosystem services that related to soil health, including plant growth regulation, continuous cropping barrier reduction, water quality improvement, human health maintenance, climate change mitigation, and soil carbon sequestration, suggesting the important roles of soil microbiome for soil health. In addition, we review the development of soil microorganisms as indicators in soil health assessment in arid region. Meanwhile, we introduce the characteristics of soil microbiome in arid region and their responses to environment stresses, particularly drought. Besides, the research progresses of soil health in arid regions are summarized. Finally, we prospected key research questions of soil microbiome and soil health in arid region, and provide new insights for applying soil microbial resources to maintain and improve soil health in arid regions.