This study presents a computational investigation into the migration behavior of organic contaminant in natural clay sites. The presented methodology incorporates multiphase flow, interphase mass transfer, and adsorption processes to characterize the time-varying distribution of organic contaminants. Drawing on damage theory, a novel organic corrosion hydraulic constitutive law is introduced to quantify the corrosion degree of organic contaminants on the meso-scale fabric of clays (e.g., macro pores and aggregates). The proposed corrosion constitutive relationship can predict the dynamic evolution of permeability in organic-contaminated clays with saturation and contaminant types. Model validation is achieved through comparison with unit and sequential permeation experiments, demonstrating a good agreement with experimental data. The results indicate that neglecting the effects of organic corrosion leads to a significant underestimation of both horizontal and vertical contaminant migration distances. Notably, the horizontal migration distance of contaminants is found to exceed the vertical migration distance. These findings highlight the significance of organic corrosion in influencing the contamination migration in clay sites.