The croplands in arid regions are characterized by saline-sodic soils, low content of soil organic carbon (SOC), and large proportions of soil inorganic carbon (SIC). Both SOC and SIC are influenced by agricultural management. However, it remains unclear that how the stock and stability of SOC and SIC at different soil depths vary after long-term fertilizations. We investigated the vertical patterns of soil carbon (C) change and SOC stability in six fertilization treatments (e.g., CK, NPK, N2P2K, NPKS, NPKS2, and NPKM) in the Fukang Station for Desert Ecological Research, Chinese Academy Sciences. The results showed that:(1) The contents and stocks of SOC in the tilled layer (0-20 cm) increased after 31-year fertilizations, especially in the treatment of chemical fertilizer combined with straw returning, which could be due to high plant C inputs. (2) In addition, the thermal stability of SOC decreased in all the fertilization treatments, suggesting that increased SOC after long-termfertilizations might be vulnerable to environmental changes and would promote the transformation of soil nutrients. (3) The contents and stocks of SIC decreased in different fertilization treatments, and the decreases in SIC reduced along soil profiles, resulting in the increment of SIC to the depth of 60 cm, which might be caused by irrigation. (4) Despite the increases in SOC after the long-term fertilizations, the decreases in SIC led to the loss of soil total C, demonstrating that the changes in SIC determine the net changes in soil C in the arid regions. Overall, the results of this study suggest to estimate accurately the changes in soil C in the arid regions, we need to understand changes in both SOC and SIC and their stabilities at different soil depths.