Soil inorganic carbon (SIC), a predominant carbon (C) reservoir in arid ecosystems, is conventionally viewed as geogenic and inert on biological timescales. Whether and how contemporary plant-fixed C actively contributes to this pool remain unresolved, creating a critical gap in our understanding of the terrestrial C cycle. Here, we traced the fate of photosynthetic C via in-situ(13)CO(2) pulse-labeling of the deep-rooted subshrub Alhagi sparsifolia in a hyper-arid desert ecosystem on the southern fringe of the Taklimakan Desert. We detected significant and persistent C-13 enrichment in both soil organic C (SOC) and SIC pools throughout the 0-200 cm profile over 360 days. The incorporation of photosynthetic C into SIC was strongly correlated with biomarkers of living microorganisms (i.e., phospholipid fatty acid-C-13) and the abundance of functional genes such as carbonic anhydrase (can). Random forest and correlation analyses identified nutrient availability (available phosphorus, available potassium, and nitrate nitrogen), rather than Ca2+ and pH, as the primary regulator of this microbial-mediated C flow. Shallow soils (0-60 cm) were hotspots for rapid C transformation, while deeper layers (60-200 cm) acted as a long-term SIC sink. Our study offers evidence consistent with an active, microbially driven pathway that transfers atmospheric CO2 fixed by plants into the stable SIC pool. This "microbial bridge" mechanism, governed by nutrient availability, reveals a previously overlooked but potentially rapid biological component of C sequestration in drylands, with profound implications for global C cycle models.