Soil aggregate stability is an important index for predicting soil water loss and soil erosion resistance. Plant roots effectively control soil erosion and stabilize soil structure, which has a crucial influence on the formation of aggregates and soil organic carbon (SOC) sequestration. We examined how rhizosphere effects influence soil aggregate stability and its associated SOC contents and δ13C values, following a proposed extended model of carbon (C) flows between the aggregate size classes in the root systems based on 13C fractionation in each step of SOC formation. The results show that the rhizosphere effects significantly improved the stability of aggregates. The mean weight diameter (MWD) and geometric mean diameter (GMD) of rhizosphere soil aggregates were significantly higher than those of non-rhizosphere soil aggregates associated with plants with fibrous roots. SOC levels of all size aggregates in the rhizosphere soil of both fibrous and tap root plants were higher than those of nonhizosphere soil. Moreover, SOC contents increased in the order of silt-clay particles (SCP, <0.05 mm),microaggregates (MIA, 0.05-0.25 mm) and small macroaggregates (SMA, 0.25-1 mm), and then decreased from SMA to large macroaggregates (LMA,> 1 mm). The δ13C values in non-rhizosphere soil were generally higher than those in rhizosphere soil in  ggregates of the same size class, especially in the tap root plants. Except for the rhizosphere soil of fibrous root plants, the other three soil types (rhizosphere and non-rhizosphere soil of tap root plants, and non-rhizosphere soil of fibrous root plants) were shown to have aggregate δ13C values that decreased with increasing soil aggregate size. Δ13C enrichment of the SOC fractions showed that the general flow direction of SOC was from rhizosphere to non-rhizosphere, and from large aggregates to small aggregates. The C flow in the aggregates of rhizosphere soil was clearly greater than that in the non-rhizosphere soil, especially with the fibrous root plants. These findings suggest that plant roots have the potential to regulate soil structural stability,and enhance soil erosion resistance and SOC sequestration.