Grassland desertification is an important issue in grassland areas. Desertification process not only results in the appearance of wind-sand landscapes on the surface, but also causes a significant reduction in vegetation cover and soil production potential. Grassland as an important carbon and nutrient reservoir, desertification process may also have important impacts on the changes of soil carbon and nitrogen pools. To investigate the influence of soil carbon and nitrogen storage during alpine grassland desertification, this study used spatial sequences instead of temporal succession to investigate the variations of soil carbon and nitrogen storage in different depths and the variation patterns of productivity and soil physicochemical properties during alpine grassland desertification in the northern Xizang plateau. The results showed that: (1) The lightly, moderately and severely deserted grasslands showed no change in soil total carbon and total nitrogen storage, while extremely severely deserted grasslands led to sharp carbon and nitrogen loss (69% and 55% decrease, respectively, P ＜ 0.05). (2) Above-ground biomass of the community gradually decreased with the aggravation of the degree of desertification, and the root biomass of severe and extremely severe desertification grassland decreased significantly (47% and 99%, respectively, P ＜ 0.05). Soil bulk density and gravel content showed gradual increases with the increase of desertification, while total carbon, total nitrogen content and water content gradually decreased, indicating that the desertification process led to coarse-grained and infertile soils. (3) The Shannon diversity index and Chao1 richness index of soil bacteria showed increasing trends with increasing desertification gradient, with significant differences in the severe heavy and heavy desertification gradients, while these two indices of soil fungi did not show significant differences along with the desertification gradient. (4) We used structural equation modeling to explore the factors that drove changes in soil total carbon and nitrogen stocks during desertification process in alpine grasslands. The key factors affecting soil carbon storage were mainly soil physicochemical properties, such as soil gravel ratio, soil water content as well as plant aboveground productivity, while those affecting soil nitrogen storage were soil gravel ratio, water content, and soil microbial richness. In conclusion, the factors affecting soil carbon and nitrogen storage during desertification process in alpine grassland were mainly soil physicochemical properties, while plant community production had less influence. Moreover, soil carbon and nitrogen stocks during the desertification process showed a sharp decrease in the transition from heavy to extremely heavy desertification, so the early protection of potentially desertification alpine grassland is more conducive to the maintenance of soil carbon sinks.