As an important part of healthy ecosystem in arid and semi-arid areas, biological soil crust (BSC) has many ecological functions, such as carbon and nitrogen fixation, reducing soil water evaporation and soil runoff. These functions are closely related to the species and coverage of BSC. In view of this, BSC plays an important role in maintaining the stability of desert ecosystem. Therefore, taking the scale of remote sensing data into account and quantifying the environmental factors that affect the distribution patterns of BSC are the key to ecological restoration and governance of desertification land. The environmental factors that affect the BSC coverage are complex. There were two limitations in the existing research methods. On the one hand, most of the researches were small-scale analysis between BSC and environmental factors in the field. On the other hand, Numerous studies focused on analyzing the one-way relationships between BSC and environmental factors in isolation. In our research, to systematically sort the interactions among the distribution of BSC, vegetation, and soil, the structural equation modeling (SEM) which is a comprehensive method was used. The paths among BSC coverage, vegetation coverage, soil pH, salinity, organic matter, and particle size on a 30-meter pixel scale were analyzed. The results showed that:(1) in the Mu Us Sandy Land, BSC coverage is affected by various environmental factors and cannot be explained by a single variable. The BSC coverage was greatly and positively correlated with vegetation coverage, soil organic matter, average particle size, and the ratio of fine particles (P< 0.01), and negatively correlated with the ratio of coarse particles (P< 0.01). (2) BSC coverage and vegetation coverage interacted with each other through organic matter. BSC coverage had a positive effect on vegetation coverage (path coefficient=0.43, P>0.05). Vegetation coverage had a negative effect on BSC coverage (PC=-0.22; P >0.05). (3) the average particle size and the proportion of fine particles were all positively affected on BSC coverage. Among them, the average particle size had a great impact on the coverage of BSC (PC=0.67; total effect value=0.590). The proportion of fine particles had an indirect impact on BSC coverage (indirect effect value=0.052). (4) the salinity significantly and negatively impacted BSC coverage (PC=-0.41, P< 0.05). The value of soil pH had a little positive effect on BSC coverage (total effect value=0.072). The results provided scientific evidence for BSC detection, protection, and restoration, as well as the basis for policymaking to restore the desert ecosystem.