Preferential flow processes are controlled by subsurface structures with the hierarchical organization across scales, but there is a lack of multiscale model validation using the field data. In this study, using a comprehensive dataset collected in the forested Shale Hills catchment, we tested and validated preferential flow occurrence by 2-dimension HYDRUS-2D at the hillslope scale, and in comparison, with 1-dimension HYDRUS-1D at the pedon scale and 3-dimension HYDRUS-3D at the catchment scale. There was good agreement between the 1D simulations and measurements of soil moisture in the soil profile, which was mainly affected by the vertical change in porosity/permeability with depth and precipitation characteristics; however, short-term fluctuations due to preferential flow were poorly captured. Notably, 2D and 3D simulations, accounting for preferential flow controlled by slope positions and shallow fractured bedrock, provided better results than the 1D simulations. Furthermore, a dual-porosity or anisotropic model provided more accurate predictions of soil moisture than a single-porosity or isotropic model due to a more realistic representation of local soil and fractured shale structure, which is also the premise of preferential flow (PF) occurrence. Consequently, our study reflected the central importance of multi-dimensional model approaches while highlighting the quantification of the soil structure and fractured nature of the bedrocks itself is essential to the simulation of preferential flow. The multi-dimensional modeling approaches can provide the mechanic presentation of PF pathways to the first-order stream and the necessity of the 3D simulation with detailed information to identify the dominant hydrological process.