δ¹³C enrichment (Δ δ¹³C) is an effective indicator to reflect the temporal dynamics of soil organic carbon (SOC) stock which is usually difficult to detect due to the slow turnover rate of SOC; however, because of the rare simultaneous measurements of both plant and soil δ¹³C, it is usually difficult to explore the geographic variations and controlling factors of Δ δ¹³C (δ¹³C of surface soil subtracting that of plant leaf). In this study, plant leaf δ¹³C, soil δ¹³C, and Δ δ¹³C were investigated along steep climatic and edaphic gradients to improve the understanding of SOC dynamics in deserts of northern China. Both soil δ¹³C and plant leaf δ¹³C decreased with mean annual precipitation (MAP), and soil δ¹³C was positively related to plant leaf δ¹³C and was higher than plant leaf δ¹³C across all C₃ plant-dominated deserts (Alkaline soil desert, Gobi desert, alpine desert, and temperate steppe desert) except C₄ woody shrub-dominated sandy desert. Δ δ¹³C was positively related to the SOC and soil silt contents across the C₃-dominated desert transect, suggesting a faster decomposition of SOC at higher Δ δ¹³C sites. The shrub importance value index in the plant community enhanced Δ δ¹³C by increasing the soil silt and SOC contents in both steppe and alkaline soil deserts, indicating that shrub encroachment can increase the SOC content and SOC decomposition. Our results indicate that shrub colonization not only increases SOC content but also regulates SOC decomposition via changing vegetation cover and edaphic variables.