Permeable reactive barrier (PRB) remediation technology has been widely used in the remediation of groundwater contamination. In numerical simulations, neglecting the non-uniform distribution of heavy metal contamination along the depth may lead to deviations between simulation results and reality. The distribution of heavy metals in the soil layer around a non-ferrous mining area in Hezhou, Guangxi, southern China was investigated, and it was found that the standard Gaussian function could well describe the non-uniform distribution of heavy metals in the soil layer. A two-dimensional analytical model solved by the finite element method was used to simulate the migration process of heavy metal contamination in the aquifer and PRB. The results show that the uniform distribution of contaminants along the depth ignores the dilution effect, which may underestimate the service life of the PRB and lead to an overly conservative design of the PRB. The breakthrough time of the PRB decreases with the increase of the maximum initial concentration (Cin,max) and the high concentration range (σ), and increases almost linearly with the barrier thickness (Lw). An optimal design method for PRB location and thickness is proposed, which can provide a reference for the engineering application of PRB.