Soil inorganic carbon (SIC) exerts a strong influence on the carbon (C) sequestered in response to nitrogen (N) additions in arid and semi-arid ecosystems, but limited information is available on in situ SIC storage and dissolution at the field level. This study determined the soil organic/inorganic carbon storage in the soil profile at 0–100 cm depths and the concentration of dissolved inorganic carbon (DIC) in soil leachate in 4 N application treatments (0, 200, 400, and 600 kg N ha−1 yr−1) for 15 years in the North China Plain. The objectives were to evaluate the effect of nitrogen fertilizer on total amount of carbon sequestration and the uptake of atmospheric CO2 in an agricultural system. Results showed that after 15 years of N fertilizer application the SOC contents at depths of 0–100 cm significantly increased, whereas the SIC contents significantly decreased at depths of 0–60 cm. However, the actual measured loss of carbonate was far higher than the theoretical maximum values of dissolution via protons from nitrification. Furthermore, the amount of HCO3 − and the HCO3− /(Ca2++Mg2+) ratio in soil leachate were higher in the N application treatments than no fertilizer input (CK) for the 0–80 cm depth. The result suggested that the dissolution of carbonate was mainly enhanced by soil carbonic acid, a process which can absorb soil or atmosphere CO2 and less influenced by protons through the nitrification which would release CO2. To accurately evaluate soil C sequestration under N input scenarios in semi-arid regions, future studies should include both changes in SIC storage as well as the fractions of dissolution with different sources of acids in soil profiles.