Groundwater can be stored abundantly in granula-composed aquifers with high permeability. The micro-structure of granular materials has important effect on aquifer permeability; and the contaminant migration and remediation in aquifers is also influenced by the characteristics of porous media. In this study, two different microscale arrangements of sand particles are examined to reveal the effects of micro-structure on the contaminant migration and remediation. With the help of fractal theory, the mathematical expressions of permeability and entry pressure are conducted to delineate granular materials with regular triangle arrangement (RTA) and square pitch arrangement (SPA) at microscale. Using Sequential Gaussian Simulation (SGS) method, a synthetic heterogeneous site contaminated by Perchloroethylene (PCE) is then used to investigate the migration and remediation affected by the two different micro-scale arrangements. PCE is released from an underground storage tank into the aquifer and the surfactant is used to clean up the subsurface environment. Results suggest that RTA not only can cause larger range of groundwater contamination, but also can cause harder remediation for contaminated aquifer. The PCE remediation efficiency of 60.01 %–99.78 % with a mean of 92.52 % and 65.53 %–99.74 % with a mean of 95.83 % are achieved for 200 individual heterogeneous realizations based on the RTA and SPA, respectively, indicating that the cleanup of PCE in aquifer with SPA is significantly easier. This study leads to a new understanding of the microstructures of porous media and demonstrates how micro-scale arrangements control contaminant migration in aquifers, which is helpful to design successful remediation scheme for underground storage tank spill.