Abstract: The specific effects of the long-term addition of exogenous organic materials on the soil inorganic carbon pool in farmlands remain unclear. Our study determined the effects of different fertilization regimes on the soil carbon pool distribution and related physicochemical properties based on a 16-year long-term experiment in North China. Six treatments were established: control (CK), nitrogen fertilizer (N), chemical fertilizer (NPK), nitrogen fertilizer combined with organic fertilizer (MN), chemical fertilizer combined with organic fertilizer (MNPK), and chemical fertilizer combined with straw (SNPK). This study comprehensively analyzed the effects of different fertilization treatments on soil organic carbon (SOC) and soil inorganic carbon (SIC) contents, and other key soil physicochemical properties. Principal component analysis was used to investigate the effects of the addition of exogenous organic material on changes in the soil carbon pool. The results showed that the SOC content in 0–20 cm soil layer increased by 45% on average with the long-term addition of exogenous organic materials compared with CK. The MNPK treatment increased the SIC content by 21% in the 40–50 cm soil layer, whereas the SNPK treatment reduced the SIC content by 28% in the 50–60 cm soil layer. Soil pH and water conditions were the key factors affecting SIC change; and SOC content, organic material input, soil parent material, and other factors affect the process. Specifically, straw decomposition produces organic acids and CO₂ and promotes the mineralization of native SOC to generate more CO₂, subsequently leading to a significant decrease in soil pH. This is the primary reason for the significant loss of deep SIC under SNPK treatment. In conclusion, fertilizer combined with organic fertilizer is conducive to the accumulation of soil organic and inorganic carbon, whereas fertilizer combined with straw may lead to a loss of inorganic carbon in deep soil. This provides a theoretical basis for revealing the transformation mechanism of the soil carbon pool after the addition of exogenous organic materials as well as has important significance for evaluating the key role of SIC in soil carbon storage.