Soil organic carbon (SOC) sequestration and protection not only mitigate CO2 emission but also promote soil fertility. Naturally, calcareous soils in the karst area contain significantly higher SOC concentration than the red soils in non-karst area of the same region. After cultivation, calcareous soils are susceptible to SOC loss, with substantial SOC loss occurring within two years. However, the underlying mechanisms are not well understood. To expand our understanding of the process of rapid SOC loss and the role played by soil aggregate disruption, we conducted a 1-year in situ study in a karst area in Southwest China. We tilled the soil at different intervals—every 6 (T1), 4 (T2), 2 (T3), and 1 (T4) months—causing aggregate disruption of different intensities. No-tillage soil (T0) was treated as a control. After 1 year, the SOC concentration in the soil under the tillage treatments (T1, T2, T3, and T4) was significantly reduced; however, in the no-tillage soil, no significant change was observed. The SOC loss within the first 3 months accounted for approximately 70 %–84 % of the total SOC loss, indicating that SOC loss was most pronounced during the initial tillage period. SOC was mainly stored in the 2–8 mm soil aggregates. Tillage-induced disruption of the 5–8 mm aggregates resulted in a decline of the physical protection of SOC, leading to substantial SOC loss from these aggregates. Besides, the SOC loss was positively correlated to the amount of Ca2+ leaching, indicating that enhanced carbonate dissolution might contribute to the decline in aggregate stability and associated SOC loss. Our results emphasize the importance of zero-tillage management and maintenance of large soil macroaggregates for sustainable land use of calcareous soils in karst regions.