Ephemeral plants and xerophyte develop an obvious gradient change of population in the east-west direction of Gurbantunggut Desert. Whether the microorganism of the algae crust soil has the similar distribution characteristics like that? This paper discusses the bacterial and fungal community structures distribution characteristics of algal crust soil in the east-west direction of the desert by using high-throughput sequencing technology. We tested physical and chemical factors of the algae crust soil samples which were collected separately in the western, middle, and eastern regions of desert and compared the spatial differentiation of soil properties. Then, we conducted the bacterial and fungal amplicon sequencing, so as to analyze the microbial communities differentiation in different regions of the desert and the correlation between microbial diversity and environmental factors. At last the function was predicted according to the types of microorganism. The results indicate that there are significant differences in soil total nitrogen (TN), total phosphorus (TP), total potassium (TK), pH and C:P and N:P in algae crust soil, with fewer gradient changes of other indicators regarding spatial scale of the desert. According to the alpha diversity of microorganism, there are significant differences in the bacterial communities' richness and diversity in three regions, among which the diversity of east and west regions are obviously differentiated. However, there is no significant difference in α-diversity indexes of the fungi, whose community structure is relatively uniform without differentiation. The β-diversity results present that the bacterial communities are significantly different between the western and eastern areas, while the middle of the desert is the transition zone. At the phylum level, the dominant bacterial populations are Cyanobacteria, Proteobacteria and Bacteroidetes, and fungi are mainly Ascomycota and Basidiomycota. From the perspective of the genus of bacteria, top 30 in genus abundance appear different microbial community structure. From the Spearman analysis result, several physical and chemical factors are positively correlated with algal crusts microbial community. In addition, the clustering relationship of bacterial functional genes in the middle and west of the desert is closer, and having significant difference with some functional genes in the east. However, fungal community functions don't have significant difference in different regions of the desert. This paper finds that the change of soil properties have caused divergence of bacterial communities in the eastern Gurbantunggut Desert, adaptive differentiation significantly occurring in the central and western regions and some gradually differentiated functional genes. However, these changes can't lead to significant differentiation of fungal community structure and function.