Saline-alkali soil is an important soil inorganic carbon pool in terrestrial ecosystems, but changes in soil physicochemical properties during organic amendment are bound to affect the dynamic balance of inorganic carbon. In this study, vinegar residue was used as an exogenous organic material in a two-year field positioning experiment to investigate the changes in soil inorganic carbon (SIC) and their dominant controlling factors during organic amendment in coastal saline-alkali land. The results showed that vinegar residue application significantly reduced SIC content in the 0–40 cm soil layer, with the maximum reductions in the 0–20 cm (surface) and 20–40 cm layers reaching 24.3% and 15.3%, respectively, while the proportion of carbonate minerals in the surface soil decreased by 2.32%. Meanwhile, the contents of dissolved inorganic carbon (DIC) and soil organic carbon (SOC) in the surface layer increased significantly by 94.40% and 219.46%, respectively, indicating that carbonate minerals underwent marked dissolution. Further analysis revealed that the reduction in SIC did not simply represent carbon loss, but was accompanied by increased DIC, decreased pH, and reduced bulk density, driving the downward migration of dissolved inorganic carbon, potentially leading to vertical redistribution of soil inorganic carbon and forming a potential deep carbon sink. Stepwise regression and random forest analysis confirmed that DIC, pH, and bulk density were the dominant factors regulating SIC changes. This study reveals the redistribution mechanism of inorganic carbon pools in saline-alkali land under organic amendment, providing a theoretical basis for the synergistic management of fertility improvement and carbon sequestration in coastal saline-alkali soils.