The topsoil of smelter sites is subjected to severe contamination by heavy metals (HMs). Existing numerical simulations typically treat soil and groundwater separately owing to data limitations and computational constraints, which does not reflect the actual situation. Herein, a three-dimensional coupled soil-groundwater reactive solute transport numerical model was developed using the Galerkin finite element method with the smelter as the research object. This model treats soil and groundwater as a whole system, providing a quantitative characterization of HMs migration patterns in soil and groundwater. The model used the reaction coefficient (λ) and retention coefficient (R) to describe the release and adsorption capacities of HMs. Results from the model were consistent with actual pollution distributions in the field, indicating the efficacy of the soil-groundwater remediation technology for severe soil and localized groundwater pollution. The constructed three-dimensional coupled soil-groundwater reactive solute transport model can describe and predict the distribution and transport diffusion behavior of HMs at the study site with good efficacy. The model was also used to simulate and predict the effects of remediation technologies during the treatment of smelting site contamination, providing guidance for optimizing the treatment plan.