Microbiological mixed DNA (genomic DNA) was directly extracted from soil in the Gurbantunggut desert. Using Illuminamiseq sequencing platform, diversity of community structure was analyzed from the bacterial 16S rDNA. The research showed that: 1) Because of the low quantity of microbe in desert vegetation soil and the low activity, there were many difficulties in the DNA extraction; 2) In total, measured sequences belonged to 23 phyla and 316 genera, among them, some sequences were uncultured groups that had an uncertain affiliation, which had been submitted to the GenBank PEMBL PDDBJ databases under accession numbers KT984242_ KT984249. 3)There were some discrepancies between groups. The difference was affected by factors such as soil physical and chemical factors. The water content influenced the amount of Proteobacteria and Acidobacteria. The unique Elusimicrobia was the soil of plant H. ammnodendron and Tamarix ramosissima, which was closely related to the nitrogen fixing bacteria. The soil microbial biomass carbon could reflect the quantity of microorganism but not the types of microorganism.