The effects of rotation patterns on soil aggregate composition and soil organic carbon were studied in this paper in order to setup rational rotation pattern in yellow soil based on a successive 23-year field experiment, in which three treatments were chosen:maize monoculture system (MM), wheat (intercropping green manure)-maize rotation (WMR) and rape-maize rotation (RMR). The results showed that >0.25 mm aggregates were the dominant component of the mechanically stable and water stable aggregates with the proportion beyond 93.04% and 74.59% respectively. Compared with MM treatment, WMR and RMR treatments significantly improved the contents of 5-2 mm, 2-1 mm mechanical stability aggregates and the contents of >5 mm, 5-2 mm water stable aggregates; WMR treatment significantly increased MWD (mean weight diameter) of water stable aggregates by 50%; WMR and RMR treatments significantly decreased PAD (percentage of aggregate destruction) and ELT (soil aggregates unstable mass index) by 31.32%, 25.97% and 35.90%, 30.65% respectively. WMR treatment had the highest organic carbon content in different size levels of water stable aggregates, and organic carbon contents in >5, 1-0.5, 0.5-0.25 mm aggregates increased by 17.60%, 34.41% and 45.67% respectively compared with MM treatment. The contents of soil aggregate organic carbon was mainly in >0.25 mm aggregates, higher than that in microaggregate (<0.25 mm). Rotation measures mainly increased the contribution rate of organic carbon in >5 mm water stable aggregates, WMR and RMR treatments increased 23.18 and 9.16 percentage points respectively compared with MM treatment. In summary, wheat (intercropping green manure)-maize rotation can effectively improve the composition of soil aggregates, improve the stability of soil aggregates and organic carbon content, thus, is a reasonable rotation pattern in the yellow soil of Guizhou.