The relation and interaction of rhizosphere microbial communities with local environmental factors and root traits is currently a vibrant research hotspot. Yet little is known about how the morphological and functional properties of roots in steppe plants affect microbial community structure. Hence, this study investigated the rhizosphere soil of six Stipa species across the Ningxia steppe in China to examine how the composition of their microbial communities responds to both root traits as well as surrounding environmental factors. Our results reveal significant differences (p < 0.001) in the composition of rhizosphere microbial communities among different Stipa species. The dominant bacterial and fungal phyla are Proteobacteria and Ascomycota, respectively; further, Mortierellomycota plays a key role in the fungal community and is closely associated with other fungal taxa. According to the functional gene predictions for bacteria and fungi, the rhizosphere microbes associated with Stipa species are mainly related to organic matter metabolism and nitrogen cycling. We find that soil physicochemical properties (SOC, TN, TP, AP, SWC, FL, SL) and root traits (RTD, Rtn) are pivotal factors which directly influence the structure of microbial communities dwelling in the rhizosphere of Stipa species. The dominant phyla of fungi and bacteria can respond to those properties in two contrasting ways. One group, consisting of bacteria such as Acidobacteria and fungi like Mortierellomycota, has a relative abundance that is positively correlated with soil nutrients (SOC, TN, AN, TP), whereas the second group, which includes bacteria such as Bacteroidetes and fungi like Ascomycota, is characterized by a negative correlation. More importantly, our results show that root traits significantly impact (p < 0.001) fungal diversity, whereby the morphological and functional properties indirectly affect the composition of bacterial and fungal communities by modulating soil properties. Altogether, the findings suggest that the morphological and functional properties of Stipa roots play a prominent role in shaping the community structure of rhizosphere microbes in steppe, providing a theoretical basis for exploring changes in these communities across space and time, as well as offering insights for grassland conservation and sustainable management.