Preferential flow plays an important role in the ecosystem. In order to understand the influence of enclosure on the root-soil structure in the preferential flow region, and to understand the difference of root-soil structure between the preferential flow region and the matrix flow region. In this paper, the soil in the preferential flow region of Caragana korshinskii shrub under enclosure or grazing measures in Yanchi, Ningxia, China was selected as the research object. The geometric distribution and topological indexes of root-soil structure (aggregates, macropores and roots) were obtained by CT scanning and three-dimensional image processing. The results showed that the enclosed natural grassland had the highest staining area ratio (40.38%) and staining depth (271 mm). The distribution of soil aggregates and macropores in grazing artificial C. korshinskii shrub and enclosed natural C. korshinskii shrub was more uniform. Enclosure significantly reduced the number density and volume density of soil aggregates, macropores and roots in the preferential flow region (p<0.05). Compared with the matrix flow region, the number density of soil aggregates in the preferential flow region increased significantly (p<0.05), and the average equivalent diameter decreased significantly (p<0.05). Enclosure negatively affects soil aggregates and macropores. Aggregates directly promote the preferential flow process, and macropores indirectly affect the preferential flow process through aggregates. Clarifying the relationship between enclosure, root-soil structure and preferential flow can provide a basis for vegetation restoration management in arid and semi-arid areas.