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 three tillage treatments: conventional tillage with rotation of rice and winter fallow (CT-r) system, no-till and ridge culture with rotation of rice and rape (RT-rr) system, and conventional tillage with rotation of rice and rape (CT-rr) system. The results showed that the aggregates 0.02-0.25 mm in diameter accounted for the largest portion in each soil layer under all treatments. Compared with the CT-r system, in the 0-10 cm layer, the amount of aggregates >0.02 mm was larger under the RT-rr system, but smaller under the CT-rr system. In the 0-20 cm layer, the organic carbon content of all fractions of aggregates was the highest under the RT-rr system and lowest under the CT-rr system. The total organic carbon content showed a positive linear relationship with the amount of aggregates with diameter ranging from 0.25 to 2 mm. The storage of organic carbon in all fractions of aggregates under the RT-rr system was higher than that under the CT-r system in the 0-20 cm layer, but in the 0-60 cm soil layer, there was no distinct difference. Under the CT-rr system, the storage of organic carbon in all fractions of aggregates was lower than that under the CT-r system; most of the newly lost organic carbon was from the aggregates 0.002-0.02 and 0.02-0.25 mm in diameter.