Non-structural carbohydrates (NSC) are critical indicators of the carbon acquisition and consumption balance in vascular plants, and are equally important for biological soil crusts (BSCs), which serve as significant carbon sinks in arid regions. Nitrogen (N) deposition significantly alters NSC storage by affecting plant growth, photosynthesis, and the carbon-to-nitrogen ratio. However, the response of NSC to N deposition may vary across different developmental stages of BSCs due to differences in physiological structures and soil properties. We conducted a long-term field N addition experiment (2010–2021) in the Gurbantunggut Desert, with N rates from 0 to 3 g m⁻² yr⁻¹ and a 2:1 NH₄⁺-N to NO₃⁻-N ratio, to examine the effects of N on NSC and their components (fructose, sucrose, soluble sugars, and starch) in three BSC types: cyanobacterial, lichen, and moss crusts. Our results revealed that the development of BSCs from cyanobacterial to lichen and moss crusts significantly alters NSC allocation, with an increasing ratio of soluble sugars to starch (0.24–1–1.68). As N added levels rise, NSC content in all three BSC types exhibits a nonlinear trend, characterized by low promotion and high inhibition, with distinct threshold points (N1.5-N0.5-N0.5). This phenomenon arises from shifts in the NSC driving factors under N addition: transitioning from soil nutrient dependence (cyanobacteria) to regulation by plant antioxidant enzyme activity (lichen), and ultimately to a more complex physiological regulation involving photosynthetic pigments and antioxidant enzyme activities (Moss). This study reveals the transition of BSCs from “environmental adapters” to “ecological regulators” throughout their successional stages. These findings provide new insights into the C metabolism of BSCs and have important implications for ecological restoration in N-impacted arid regions. Keywords: Nitrogen deposition; Biological soil crusts; Non-structural carbohydrates; Photosynthetic pigments; Soil nutrients.