Shrub encroachment into grasslands can affects soil organic carbon (SOC). However it is unclear how and why shrub encroachment can change soil carbon. Field evidence from deep soil is lacking particularly. Soil aggregation is considered as one of the key mechanisms of carbon sequestration during the encroachment. Understanding how shrub encroachment affect soil aggregation and associated SOC is essential to clarify the effect of shrub encroachment on ecosystem carbon balance. In this study, we investigated the amount and vertical distribution of soil aggregation and associated SOC in both shrub patches and neighboring grass patches in two types of shrub-encroached grassland in Inner Mongolia to explore the impact of shrub encroachment on SOC and its underling mechanisms. The results show that there was no significant difference in the amount of total and each class of aggregate between shrub patches and grass patches. However, the content of SOC within the soil aggregate was significantly higher in shrub patches than grass patches, especially in macroaggregate for >0.25mm in typical shrub-encroached grasslands, while there was no significant difference in desert shrub-encroached grasslands. The results indicated that shrub encroachment affect soil carbon through changing SOC within macroaggregate. Further experimental verification is needed to assess the detailed relationship between aggregation and shrub encroachment.