Nematodes occupy multiple trophic levels in the soil food web, which serve as important indicators of soil ecological processes and play an important role in maintaining ecosystem structure and function. As desert engineers, biocrusts have a positive impact on the biodiversity of the arid ecosystems. However, the mechanism of their impacts on soil nematode communities has remained unanswered. We collected the sample from different soil layers (0—14 cm soil layer, every 2 cm layer) under the cyanobacteria- and moss biocrusts as well as uncrusted soil. In the laboratory, soil nematodes were extracted using Baermann funnel method and then they were counted and identified. We comparatively analyzed the effects of biocrusts types and soil depth on the richness, abundance and diversity of soil nematodes. The results showed that: (1) The Cephalobus, Leptonchus, and Microdorylaimus were the dominant nematodes in uncrusted soils, while the Alaimus, Leptonchus, Cervidellus, and Microdorylaimus were the dominant nematodes in biocrust-covered soils. (2) As compared with uncrusted soils, cyanobacterial biocrusts increased the generic richness, abundance, and Shannon index of soil nematodes by 35.2%, 89.2%, and 4.5%, respectively, while moss biocrusts increased them by 44.4%, 83.0%, and 24.8%, respectively. (3) The nematode abundance in the soil profiles covered by two types of biocrusts exhibited a unimodal distribution, with the highest nematode abundance found in the 6—8 cm soil layer, which was 3.2—11.7 times higher than the deeper soil layer. The Shannon’s index increased as the soil depth deepened, with the highest index being 1.5—1.7 times higher than the deeper soil layer. (4) Soil temperature, available phosphorus content, and organic matter content were the primary factors influencing the gennric richness of soil nematodes. Additionally, organic matter content, NH4+-N, and NO3--N content were the main factors affecting nematode abundance, while soil temperature, soil water content, and available phosphorus content were the primary factors influencing nematode diversity. In conclusion, biocrusts significantly increase the abundance and diversity of soil nematodes by enhancing soil water and nutrient content as well as by decreasing soil temperature, which further indirectly regulate the vertical distribution characteristics of soil nematode communities by influencing the vertical distribution of soil physicochemical properties. It contributes to the understanding of the maintenance and enhancement of biodiversity and ecosystem multifunctionality in arid ecosystems by biocrusts.