Mosaic distribution of shrubs with biological soil crusts (BSCs) is one of common landscape in temperate desert, which in `turn had significant effects on nutrients spatial distribution and cycling with development of shrubs and BSCs. However, our understanding about differences in response of shrubs and BSCs to nutrient as well as their contributions to variations in nutrient change at topsoil was still unclear. We used Ephedra przewalskii and moss crust as research targets, which was a dominant shrub and an advanced type of BSCs in terms of development stage in Gurbantunggut Desert, respectively. In order to explore the variation characteristics of carbon, nitrogen, phosphorus and potassium in different soil layers under different microhabitats, the contents of soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), available nitrogen (AN), available phosphorus (AP) and available potassium (AK) were determined. The results showed that, (1) Compared with bare sand, shrubs were significantly increased the contents of soil organic carbon, total nitrogen and total potassium in different soil layers of moss crusts and total phosphorus contents of bare sand, and decreased soil total phosphorus contents of moss crusts. (2) In terms of available nutrients, moss crusts reduced the contents of available nitrogen compared to bare sand in exposed areas, and increased the available phosphorus and available potassium contents. Meanwhile, moss crusts increased the contents of available nitrogen and available potassium, and decreased available phosphorus contents under shrub canopy. (3) Correlation analysis showed that available phosphorus was significantly negative correlated with available nitrogen in 0-2 cm soil layer, while significantly positive correlated with soil available nitrogen in 2-6 cm soil layer(P < 0.01). (4) Shrub explained total of 42.54% variations of soil nutrients, which was higher than that explained by moss crust (2.43%). In summary, moss crusts, and soil layers had significantly main effects on soil carbon, nitrogen, phosphorus and potassium (P<0.05), while their interactive effect was not detected (P>0.05). Compared with bare sand, shrub and moss crusts greatly improved soil carbon, nitrogen, phosphorus, and potassium at topsoil. Soil nutrients content significantly decreased with the increasing soil depths (P<0.05). All soil nutrients were inhibited under the interactive effects between shrub and moss crusts except for soil available nitrogen. Our results indicated that in desert ecosystem, soil nutrients heterogeneity at microhabitats were determined by the mosaic patch caused by drought-tolerant shrub and BSCs.