Abstract: Understanding the mechanism of fluid flow and solute transport at the pore scale is of great importance for oil recovery, crop nutrient management and groundwater pollution restoration. This study employed lattice Boltzmann model combining with GPU parallel technology to investigate the porous media of computer-generated structures and synchrotron-based X-ray micro-CT scans of soil aggregates (resolution 3.7 μm). The key parameters of fluid flow and solute transport in the porous media were obtained, and the influence of spatial heterogeneity of porous media on hydraulic properties was explored by high-performance simulation (spatial nodes up to 64 000 000). By comparing the three groups of porous media with different structures, it was found that the permeabilities of the soil sample with the highest structural complexity and beads irregularly stacked are on the order of 100 mD (i.e. 10^-13m²), which is much lower than that of the regularly stacked beads (>20 000 mD); The soil sample has a tortuosity of 1.40~1.60, which is significantly higher than that of the regularly stacked beads. Our results show that the porous media with high permeabilities have small degree of tortuosity, indicating that the permeabilities of porous media are related to the spatial heterogeneity of the structure. The permeability and tortuosity of soil aggregate are anisotropic. At given pressure gradient, the longitudinal diffusion coefficient is greater for a sample with higher permeability. The heterogeneity of the pore structure also affects the breakthrough curve. The method established in this work can simulate water flow and solute migration in real soil structure, and can be used to study the hydraulic characteristics of porous media at the pore scale.