Biochar amendments add persistent organic carbon to soil and can stabilize rhizodeposits and existing soil organic carbon (SOC), but effects of biochar on subsoil carbon stocks have been overlooked. We quantified changes in soil inorganic carbon (SIC) and SOC to 2 m depth 10 years after biochar application to calcareous soil. The total soil carbon (i.e., existing SOC, SIC, and biochar-C) increased by 71, 182, and 210% for B30, B60, and B90, respectively. Biochar application at 30, 60, and 90 t ha–1 rates significantly increased SIC by 10, 38, and 68 t ha–1, respectively, with accumulation mainly occurring in the subsoil (below 1 m). This huge increase of SIC (mainly CaCO3) is ~100 times larger than the inorganic carbon present in the added biochar (0.3, 0.6, or 0.9 t ha–1). The benzene polycarboxylic acid method showed that the biochar-amended soil contained more black carbon particles (6.8 times higher than control soil) in the depth of 1.4–1.6 m, which provided the direct quantitative evidence for biochar migration into subsoil after a decade. Spectral and energy spectrum analysis also showed an obvious biochar structure in the biochar-amended subsoil, accompanied by a Ca/Mg carbonate cluster, which provided further evidence for downward migration of biochar after a decade. To explain SIC accumulation in subsoil with biochar amendment, the interacting mechanisms are proposed: (1) biochar amendment significantly increases subsoil pH (0.3–0.5 units) 10 years after biochar application, thus forming a favorable pH environment in the subsoil to precipitate HCO3–; and (2) the transported biochar in subsoil can act as nuclei to precipitate SIC. Biochar amendment enhanced SIC by up to 80%; thus, the effects on carbon stocks in subsoil must be understood to inform strategies for carbon dioxide removal through biochar application. Our study provided critical knowledge on the impact of biochar application to topsoil on carbon stocks in subsoil in the long term.