In recent years, as one of the green coal mining technologies, coal gangue filling and coal mining technology has been widely used. The coal gangue filling body in goaf may be in an acidic or alkaline mine water environment for a long time, and the rich heavy metal elements in coal gangue may pollute the groundwater environment. In order to predict the migration distance of heavy metal elements in the goaf floor more accurately, this paper first designed the coal gangue static immersion experiment. By using ICP, the concentration of heavy metal elements in the soaking solution was tested, and then the permeability stress sensitivity of mudstone was tested. Finally, based on the above experimental results, the numerical simulation model for migration of heavy metals in coal gangue under the condition of seepage-stress coupling was established by using COMSOL multiphysics, and the concentration distribution and seepage law of heavy metals in the mudstone floor of goaf were analyzed with Mn element as an example. The research results showed that the heavy metals with pollution risk in coal gangue soaking liquid were beryllium (Be) and manganese (Mn). The diffusion distance of heavy metal elements in all stress states was 9.537 m when using the traditional model. When calculating after combining with the modified model of permeability stress sensitivity analysis, when the stress states were 0 MPa, 3 MPa, 6 MPa, 9 MPa, 12 MPa and 15 MPa, the diffusion distance of heavy metal elements was 9.326 m, 6.748 m, 5.9 m, 5.657 m, 5.558 m and 5.55 m, respectively, and the reduction rate was 2.21%, 29.24%, 38.14%, 40.68%, 41.72% and 41.80%, respectively. The migration and concentration distribution of heavy metal elements were predicted more accurately, which provided a basis for predicting and evaluating the impact risk of coal gangue on groundwater in filling coal mining goaf.