Biocrusts are a functional unit in arid and semiarid areas, their development has significant recruitment and screening effects on soil microbial communities. Microbial composition of biocrusts exhibits significant geographical patterns, but the regulation of biocrust development on the geographical patterns in unclear. In this study, we examined bacterial communities from cyanobacterial-lichen and moss crust soils in five desert habitats in northern China, and evaluated the relative importance of environmental factors and biocrust development versus geographic distance to the distance–decay relationship. To explore the effects of the sampling scale on geographical patterns, we also examined soil bacterial communities along the slope of sand dunes. Across the five desert habitats, bacterial α-diversity, phylogenetic diversity, and the dominant bacterial phyla in cyanobacterial-lichen crusts did not increase consistently with precipitation increase, instead bacterial community composition was mainly impacted by soil nutrients (SOC, TP) and biocrust development (thickness, cover and Chl a). Bacterial β-diversity in both cyanobacterial-lichen and moss crusts showed strong distance-decay relationships across the landscape scale; bacterial community composition in cyanobacterial-lichen crusts differed significantly among five desert habitats. Environmental and biocrust development variables explained bacterial community variation better than geographic distance, suggesting a weaker influence of dispersal limitation on the bacterial communities in biocrusts. In addition, the distance-decay rate was higher at the slope than that at the landscape scale, suggesting a fast turnover rate of bacterial community communities induced by topography. Our study implies that soil attributes and biocrust development have more profound impacts on soil bacterial communities than precipitation, which provides novel insights into the geographical distribution and assemblage of soil bacterial communities in deserts. Moreover, our study is significant with respect to understanding the potential responses of soil microbial communities to climate change in desert areas under the scenario of increasing precipitation variation.