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1. Different types of steppes could provide heterogeneous habitat environments for underground microorganisms, but much less is known about how soil microbes fit the distinct habitats and what are the underlying mechanisms in shaping their community patterns. 2. We simultaneously examined the community compositions and structures of soil bacteria, fungi, and diazotrophs across desert, typical, and meadow steppes in Inner Mongolia using high‐throughput sequencing. 3. The results showed that soil bacteria, fungi, and diazotrophs exhibited different distribution patterns across steppe types. Although different steppes displayed obvious differences in climate conditions, plant traits, and soil properties, most of bacterial species were shared by all the steppes while only a few species were unique, indicating that the soil bacterial compositions were hardly influenced by the steppe types. Nevertheless, the habitat heterogeneity could cause shifts in the relative abundance of some bacterial groups, which resulted in significant changes in the community structure of soil bacteria across steppes. However, the fungal community compositions and structures were similar in typical and meadow steppes but that in desert steppe were significantly different. Whereas, the community compositions and structures of diazotrophs were strongly related to the steppe types. In this study, the similar parent material backgrounds of the steppe soils might be the important factor in shaping the homologous bacterial compositions. However, the variations in soil fertility, soil water repellency, and plant species across steppes would be the major driving forces in regulating the compositions and structures of fungal communities, while the diazotrophic communities would be more closely related to the changes in plant traits and soil fertility among steppes. 4. Our results provided evidence of habitat specificity for different microbial groups and their underlying drivers. [ABSTRACT FROM AUTHOR]