To measure and manage plant growth in arid sandlands, improved understanding of the spatial patterns of desert soil resources and the role of soil microbes is required. The rhizosphere soils of Ephedra przewalskii, Reaumuria songarica, Sympegma regelii, Nitraria sphaerocarpa, and Salsola passerina in Anxi Extreme-arid Desert National Nature Reserve in Gansu Province, China were collected in July 2015. Soil microbial community structure in the rhizosphere of the studied five plants was analyzed by phospholipid fatty acid (PLFA) combined with Sherlock microbial identification system. The results showed that soil microbial PLFA species and composition in rhizosphere of five desert plants were significantly different. The characterizations of gram-positive bacteria 18:0 iso, 16:0 iso and 17:1 iso ω9c were unique in rhizosphereof R. songarica and S. passerina, respectively. 18:1 ω7c 10-methyl that indicated actinomycetes only existed in the rhizosphere of S. passerina. The total PLFA, fungi, actinomycetes and fungi/bacteria were the highest under S. passerina. However, gram-positive and gram-negative bacteria were significantly higher under E. przewalskii and S. passerina than under the other plants. AM fungi had the highest value under S. regelii. Structural equation model analysis indicated that compared with plants, soil factors had more significant effects on microbial community structure. Easily extracted glomalin had a significant effect on actinomycetes. Soil available nitrogen was the major influencing factor of gram-positive and gram-negative bacteria. Moreover, soil microbial community structure can be used to monitor soil degradation in rhizosphere soil of different desert plants.