China's western Ordos is a distribution area for the extremely precious remnants of ancient Asian environments, which in endangered plant species and complex ecosystems. Accordingly, in this study, we collect three endangered plants belonging to the Zygophyllaceae family, namely Tetraena mongolica, Sarcozygium xanthoxylon, and Nitraria tangutorum Bobr. High-throughput sequencing technology was applied to study microbial diversity in these plant rhizosphere soils. Analysis of species composition abundance, Alpha diversity, Beta diversity and microbial structure are analyzed. 2428 bacterial OTUs and 1256 fungal OTUs are obtained from the rhizosphere soils, and the bacterial and fungal sequencing coverage is above 99%. Bacilli are the most abundant (86.91%) in the bacterial community. The fungal community has significant differences in three plants. The abundances of the genus Dothideomycetes in the rhizosphere soils of Tetraena mongolica and Sarcozygium xanthoxylon plants are the highest, which are 44.57% and 37.69%, respectively. Thus, Dothideomycetes is the dominant bacteria in the community. The genus Sordariomycetes in the rhizosphere soil is the dominant fungi with a relative abundance of 41.04%. Redundancy analysis revealed that microbial communities were closely related to environmental factors. Overall, this study bring new insights into the relationship between rhizosphere soils microbial diversity and environment to improving the adaptability of the endangered plants in survival environment.