As a critical factor governing pollutant migration rates, soil saturation directly influences the long-term impermeability and contaminant retention efficacy of clay liners in landfills. To elucidate the impact of saturation-dependent mechanisms of pollutant transport in practical clay liners, a dynamic coupled model for contaminant migration in unsaturated soils was developed in this study. Based on mass and energy conservation principles, the generalized Darcy’s law was integrated into the framework, while dynamic variations in soil transport properties and physical characteristics were rigorously accounted. The governing equations for unsaturated soil consolidation, pore water flow, heat transfer, and contaminant transport were systematically formulated to establish the multi-physics model. Numerical simulations of the constructed model were conducted using the finite element analysis platform COMSOL Multiphysics, with case studies implemented to validate the model's rationality in civil engineering scenarios. Further analysis was conducted on the temporal evolution patterns of pore fluid pressure, contaminant concentration, and soil settlement under variations in saturation. Results demonstrate that pore fluid pressure transitions from shallow negative pressure to global negative pressure during consolidation, with 1–4 kPa higher pressure values being observed under high-saturation conditions (Sr > 0.85) compared to medium-low saturation cases; Solute migration rates were found to increase by 10%–25% with elevated saturation, exhibiting nonlinear attenuation with depth; Soil settlement, characterized by a nonlinear trend, peaked at approximately one year, where 5%–10% greater maximum settlement was recorded in high-saturation scenarios (Sr > 0.85) than in low-saturation cases.