The distribution of a mosaic of biological soil crusts (BSCs) and shrubs is a common landscape surface feature in temperate deserts. With the continued climatic change, the desert shrub experiences varying rates of mortality which has serious negative impacts on soil structure and functions. However, it is not clear whether BSCs, which develop extensively in areas under shrub canopies, can mitigate the effects of shrub mortality on soil nutrient multifunctionality. Therefore, in this study, the Gurbantungut Desert, a typical temperate desert in northern China, was selected as the study area, and the dominant shrubs, Ephedra przewalskii shrub, and the moss crust were used as the study objects. Soil samples were collected from the bare sand and moss crusts under the living shrub and the dead shrub and analyzed to determine their carbon, nitrogen, phosphorus, and potassium contents. The results showed that the shrub mortality reduced the soil moisture content, pH, electric conductivity, and carbon, nitrogen, phosphorus, and potassium contents in the bare sand compared with the bare sand under the living shrub. The presence of the moss crust greatly mitigated the negative impacts of shrub mortality on soil carbon, nitrogen, phosphorus, and potassium contents, and the nutrient multifunctionality of the moss crust was only reduced by 4.01% compared with the reduction by bare sand (67.42%) after shrub mortality. The results of SEM analysis showed that with the coexistence of shrubs and crust, the effect of shrubs on soil multifunctionality was much stronger than that of the moss crust; compared with available nutrients, the total nutrient content was the most important factor driving changes in soil nutrient multifunctionality. In conclusion, in desert ecosystems with degraded shrubs, moss crusts can mitigate the reduction in soil nutrient contents caused by shrub degradation and, therefore, maintain the soil stability and nutrient multifunctionality as a “substitute”.