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Soil organic carbon (SOC) sequestration in aggregates under land use change have been widely concerned due to intimate impacts on the sink (or source) of atmospheric carbon dioxide (CO2). However, the quantitative relationship between soil aggregation and SOC sequestration under land uses change has been poorly studied. Distribution of aggregates, SOC contents in bulk soils and different size aggregates and their contributions to SOC sequestration were determined under different land uses in the Puding Karst Ecosystem Observation and Research Station, karst Critical Zone Observatory (CZO), Southwest China. Soil aggregation and SOC sequestration increased in the processes of farmland abandonment and recovery. SOC contents in micro-aggregates were larger than those in macro-aggregates in restored land soils, while the opposite results in farmland soils were obtained, probably due to the hindrance of the C-enriched SOC transport from macro-aggregate into micro-aggregate by the disturbance of agricultural activities. SOC contents in macro-aggregates exponentially increased with their proportions along successional land uses. Macro-aggregates accounted for over 80% on the SOC sequestration in restored land soils, while they accounted for 31-60% in farmland soils. These results indicated that macro-aggregates have a great potential for SOC sequestration in karst soils.