Using random sampling in the field and observing the emergence of seedlings, we studied the structure, the density and vertical distribution of soil seed banks in moss crusts, lichen crusts, and bare sands in the artificially re-vegetated region of Shapotou. We found that the soil seed banks of this region were mainly composed of annual herbs and had a simple species composition and a significantly higher seed density in soil covered by biocrusts than in bare sands (P < 0.01). However, the existence of biocrusts decreased the species diversity of soil seed banks and the similarity of soil seed banks with corresponding ground vegetation. Furthermore, although the total density of soil seed was not significantly different between the two types of crusts, there were differences in the distribution within the different soil layers. Specifically, the soil seed density in the 0-2 cm soil layer of lichen crusts was significantly higher than in the corresponding layer in moss crusts (P < 0.05), while that of moss crusts was higher in the 2-5 cm and 5-10 cm soil layers. Finally, the effects of biocrusts on vertical distribution of soil seed banks varied with biocrust types. For example, germinative seeds were primarily distributed in the 0-5 cm soil layer for moss crusts and in the 0-2 cm soil layer for lichen crusts and bare sands, and their abundance decreased with soil depths. These results suggest that biocrusts increase the soil seed bank density, but also change the vertical distribution pattern of soil seed banks in artificially re-vegetated regions. A substantial proportion of small seeds are present in soil covered by biocrusts, and these seeds lack germination potential and contribute little to the above-ground vegetation. However, they play a significant role in ecosystem stability and the sustainable development of deserts.