Soil erosion alters soil structure, hydrology, and carbon dynamics, yet the mechanisms driving subsoil CO2 emissions are not well understood, particularly in the highly erodible Chinese Loess Plateau. This study investigated the effects of erosion and deposition on vertical CO2 fluxes and associated controls in 0-200 cm soil profiles of representative check dam systems. We conducted monthly measurements of CO2 flux, soil temperature, moisture, physicochemical properties, and delta 13C signatures from June to October 2022. Although total soil organic carbon (SOC) stocks were similar between erosional and depositional sites, their vertical patterns differed: SOC exhibited deeper accumulation at erosional sites but was enriched near the surface at depositional sites. Deeper soil layers (140-200 cm) in depositional sites also exhibited higher soil inorganic carbon (SIC) stocks than erosional sites, likely due to carbonate accumulation. CO2 fluxes were significantly higher at depositional sites (11.77 - 146.58 mu mol m-2 s-1) than at erosional sites (1.25 - 34.58 mu mol m-2 s-1), with subsoil emissions contributing up to 33.4 % of total fluxes. Surface CO2 fluxes were mainly influenced by temperature, SOC, and pH, while subsoil fluxes were regulated by temperature, moisture, SOC, and SIC. delta 13C signatures indicated SOC mineralization as the dominant CO2 source at erosional sites, whereas carbonate-derived CO2 was dominant in depositional subsoils. These findings reveal the crucial role of geomorphic processes and subsoil conditions in regulating CO2 emissions and provide a scientific basis for improving soil carbon management in erosion-prone regions.