Due to the unique geological background and climatic condition, karst soils in southwest China are mainly developed on carbonate rocks and accompanied by frequent dry-wet alternations. Therefore, the effects of biomass (BS) and biochar (BC) on the soil carbon pools (especially inorganic carbon) in karst regions are different from those in non-karst regions. In order to understand the responses of soil organic carbon (SOC) and soil inorganic carbon (SIC)-derived CO₂ emissions to BS and BC amendments under different water conditions in karst regions, a microscopic study under dry-wet alternate (DW) and constant moisture (CM) conditions was established to investigate the stability of BC, BS, and their effects on SOC and SIC pools by isotope double-labeling methods. Results showed that the contribution rates of SOC and SIC to soil CO₂ emissions were 51.55 %–99.52 %, 0.48 %–48.45 % and 60.55 %–97.72 %, 2.28 %–39.45 % under DW and CM conditions, respectively. Compared with the control, BS application under different water conditions increased SOC and SIC-derived CO₂ emissions by 929.78˗1443.39 % and 169.69˗335.71 %, respectively. However, BC amendment significantly decreased SOC and SIC-derived CO₂ emissions, especially in the DW condition. The mean residence time (the inverse of the decomposition rate) of BC in karst soils under different conditions ranged from 657 to 3105 years, which was much higher than those of BS (7˗18 years). Therefore, the conversion of BS to BC in karst regions enhances carbon sequestration due to its stability of recalcitrant carbon, the decrease of SOC and SIC- derived CO₂ emissions. This study is helpful to understand the quantification of CO₂ sources from calcareous soils and elucidate the environmental behaviors and carbon sequestration potentials of BC or BS amendments in karst regions.