Developing realistic soil carbon (C) sequestration strategies for China’s sustainable agriculture relies on accurate estimates of the amount, retention and tover rates of C stored in paddy soils. Available C estimates to date are predominantly for the tilled and flood-irrigated surface topsoil (ca. 30 cm). Such estimates cannot be used to extrapolate to soil depths of 100 cm since soil organic carbon (SOC) generally shows a sharp decrease with depth. In this research, composite soil samples were collected at several depths to 100 cm from three representative paddy soils in the Taihu Lake region, China. Soil organic carbon distribution in the profiles and in aggregate-size fractions was determined. Results showed that while SOC decreased exponentially with depth to 100 cm, a substantial proportion of the total SOC (30%-40%) is stored below the 30 cm depth. In the carbon-enriched paddy topsoils, SOC was found to accumulate preferentially in the 2-0.25 and 0.25-0.02 mm aggregate size fractions. d13C analysis of the coarse micro-aggregate fraction showed that the high degree of C stratification in the paddy topsoil was in agreement with the occurrence of lighter d1313C in the upper 30 cm depth. These results suggest that SOC stratification within profiles varies with different pedogenetical types of paddy soils with regards to clay and iron oxyhydrates distributions. Sand-sized fractions of aggregates in paddy soil systems may play a very important role in carbon sequestration and tover, dissimilar to other studied agricultural systems.