Stipagrostis pennata is an excellent sand-fixing plant in Xinjiang Gurbantunggut Desert, which special root sheath structure is an important embodiment of its sand-resistant adaptability. Microorganism in the root sheath is an important factor for the formation and stability of the root sheath of Stipagrostis pennata. In this study, 36 strains of bacteria, 15 strains of fungi and 13 strains of actinomycetes were isolated from the root soil samples of Stipagrostis pennata in the south and middle parts of Gurbantunggut Desert. The results showed that the predominant proportion of microorganisms in the root of Stipagrostis pennata was bacteria, fungi and actinomycetes in turn,and most of the bacteria were spherical bacteria. 22 strains were isolated which only had protease activity, only 12strains have amylase activity, there were 16 strains with both protease activity and amylase activity. 2 phosphatesolubilizing bacteria were screened from root sheath soil. In this study, the microbial resources in the root soil of Stipagrostis pennata were deeply excavated, which provided theoretical basis for the research and application of the root microbial community of sand-fixing plants.