Winter snowpack is an important source of moisture that influences the development of biological soil crusts (BSCs) in desert ecosystems. Cyanobacteria are important photosynthetic organisms in BSCs. However, the responses of the cyanobacterial community in BSCs to snowpack, snow depth and melting snow are still unknown. In this study, we investigated the cyanobacterial community composition and diversity in BSCs under different snow treatments (doubled snow, ambient snow and removed snow) and three snow stages (stage 1, snowpack; stage 2, melting snow; and stage 3, melted snow) in the Gurbantunggut Desert in China. In stages 1 and 2, Cyanobacteria were the dominant phylum in the bacterial community in the removed snow treatment, whereas Proteobacteria and Bacteroidetes were abundant in the bacterial communities in the ambient snow and doubled snow treatments. The relative abundances of Proteobacteria and Bacteroidetes increased with increasing snow depth. The relative abundances of Cyanobacteria and other bacterial taxa were affected mainly by soil temperature and irradiance. In stages 2 and 3, the relative abundance of Cyanobacteria increased quickly due to the suitable soil moisture and irradiance conditions. Oscillatoriales, Chroococcales, Nostocales, Synechococcales and unclassified Cyanobacteria were detected in all the snow treatments, and the most dominant taxa were Oscillatoriales and Chroococcales. Various cyanobacterial taxa showed different responses to snowpack. Soil moisture and irradiance were the two critical factors shaping the cyanobacterial community structure. The snowpack depth and duration altered the soil surface irradiance, soil moisture and other soil properties, which consequently were selected for different cyanobacterial communities. Thus, local microenvironmental filtering (niche selection) caused by snow conditions may be a dominant process driving shifts in the cyanobacterial community in BSCs.