Abstract: Geological disaster occurrences in loess regions are intrinsically linked to water infiltration in loess, with the Malan loess-paleosol interlayer structure significantly influencing the infiltration patterns of soil moisture. This research was carried out to reveal the moisture migration characteristics in loess-paleosol interlayers, and to investigate the influence of the moisture migration on the microstructure of loess, providing a theoretical basis for engineering practice and scientific research in loess areas. In this study, we focused on the loess of the South Plateau in Jingyang County, Shaanxi Province, and conducted water infiltration tests using a soil column model to investigate the soil moisture transport dynamics under loess-paleosol interlayer conditions. Subsequently, we analyzed the impact of soil moisture transport on the loess microstructure under these conditions through microstructural testing, and calculation of fractal dimension and probability entropy. The findings revealed that the permeability of the paleosol layer was low, causing transient water stagnation when the wetting front reached the loess-paleosol interface. The stagnant water at the interface of loess and paleosol under the influence of the paleosol layer will lead to the interconnection of pore structure, and the pore space will increase by 4.13% on average, and the analysis of the indexes of fractal dimension and probability entropy shows that the probability entropy of the pore direction decreases by 0.029 on average, and the fractal dimension decreases by 0.076 on average, i.e., the water-blocking effect of the paleosol layer makes the pore space of the loess at the interface increase, the pores are arranged in an orderly manner, and the pore morphology is regular. The results of the study provide scientific support for the engineering construction and eco-environmental protection in loess areas.