Acid in-situ leaching (ISL) is a common approach to the recovery of uranium in the subsurface. As some toxic and harmful substances might be produced by the chemical reactions among the injected sulphuric acid, the groundwater, and the porous media during leaching processes, the pollution control of the mining plan for ISL is important. In this study, a three-dimensional reactive transport modeling (3DRTM) was applied to decide the pollution control mining plan, considering the partial penetration through wellbore in confined aquifer and complex chemical reactions between main minerals. Based on the 3DRTM, different pumping ratio and non-uniform injection schemes were compared. The results show that the preferential pollution control mining plan is non-uniform injection ratio equal 0.1. By analyzing the characteristics of water table and streamline, it is concluded that the scheme has a strong hydraulic capture effect. In this scheme, the concentration of UO22+, H+, SO42- obtained by 3DRTM is lower. The inner well injection rate is 194.09 m3/d, the outer well injection rate is 158.89 m3/d, and the pumping rate is 264.00 m3/d. A reasonable suggestion is to adopt non-uniform injection mining mode in ISL.