The effect of different tillage systems on the size distribution of aggregates and organic carbon distribution and storage in different size aggregates in a Hydragric Anthrosol were studied in a long-term experiment in Chongqing, China. The experiment included five tillage treatments, which are conventional tillage with rice only system (DP), conventional tillage with rotation of rice and rape system (SH), no-till and ridge culture with rotation of rice and rape system (LM), no-till and plain culture with rotation of rice and rape system (XM) and tillage and ridge culture with rotation of rice and rape system (LF), respectively. The results showed that the aggregates 0.25-0.05 mm in diameter accounted for the largest proportion in each soil layer under all treatments. The organic carbon mainly exist in aggregates in the 0.25-2 mm and 0.05-0.25 mm diameter in the plough layer, which mainly exist in the 0.25-2 mm in diameter in the bottom layer. Distribution of organic carbon in aggregates in the 0.05-0.25 mm diameter class was highest, followed by the aggregates in the 0.25-2mm diameter class. The organic carbon in aggregates under different tillage systems was in a decreasing order of LM (21.05 g·kg-1)> DP (14.13 g·kg-1)> XM (13.29 g·kg-1)> LF (12.54 g·kg-1) > SH (11.41 g·kg-1). The total organic carbon content showed a significant correlation with the amount of aggregates with diameter >0.005 mm. The results showed that the accumulation of soil organic carbon was mainly affected by aggregates in the >0.005mm diameter class.