[Objective] Biological soil crusts can be effective in wind-preventing and sand-fixing. This is of great significance to ecological restoration in desert areas. Nevertheless, there is no literature showing a comparative analysis between the biological soil crusts and the bare sand surface layer with the same thickness or for soils beneath them.[Method] The abundance of 16S rRNA gene and the structure of bacterial communities of the moss crust layer, bare sand surface layer, and soil layers beneath them in Mu Us sandy land was analyzed by fluorescent quantitative PCR and high-throughput sequencing. Based on the data of soil physical and chemical factors, the effect of moss crust on the diversity of bacterial community in sandy land was analyzed. Also, the moss crust layer and soil layer beneath it, and the corresponding surface and underlying layers of bare sand were collected and the effects of biological crusts on soil bacterial communities and their living environments was analyzed more accurately through a comprehensive analysis.[Result] Compared with bare sand surface layer, moss crust significantly increased the contents of soil available nutrients, total nitrogen, and organic matter. Also, the contents of available nutrients, total phosphorus, and organic matter in the soil beneath moss crust were higher than those in the soil beneath bare sand surface layer. The contents of coarse silt and silt in moss crust and its underlying soil were significantly higher than those in bare sand surface layer and its underlying soil. The results showed that moss crust significantly improved the physical and chemical properties of sandy soils. Additionally, the available phosphorus, potassium, nitrogen, clay, silt, and coarse sand were important factors affecting bacterial community composition of sandy soil. The moss crust layer had the highest 16S rRNA gene copies and the bacterial abundance of moss crust and its underlying soil was significantly higher than that of bare sand surface layer and its underlying soil. The results of diversity analysis showed that the soil beneath moss crust had the highest bacterial diversity. Futhermore, the relative abundances of unclassifiled_f__Micromonosporaceae, norank_c__Cyanobacteria, and Pseudonocardia in moss crust were significantly higher than those in the bare sand surface layer. Also, the relative abundances of norank_c__Acidobacteria and Rubrobacter in the soil beneath moss crust were significantly higher than those in the soil beneath bare sand surface layer. These genera with significant differences play an important role in stabilizing the soil structure of sandy land.[Conclusion] The formation of moss crust has a significant effect on the bacterial community of the original surface and underlying soils in sandy land. This is beneficial for biological sand-fixation. This study provides an important theoretical basis for sandstorm control and desert ecological restoration in Microbiology.