Abstract: Based on identifying the hydrogeoglogical conditions of rare earth mines and determining the mining methods, the pollution sources were determined through the indoor leaching test and field test of standard ore block.The numerical simulation of the ammonia nitrogen of groundwater was taken with FEFLOW numerical simulation software, in which the biggest predictive values of the ammonia nitrogen concentration of groundwater in 4 groups were 1 076.22 mg/L, 49.18 mg/L, 0.51 mg/L and 1 400.80 mg/L respectively.The change trend and influence scope of ammonia nitrogen of the groundwater in and after the rare earth ore mining process were quantitively shown with graphical output.The research results can provide rational mining scheme for ionic adsorption rare earth in-situ leaching mining in southern Jiangxi and some references for the groundwater environment protection in mining areas, so as to realize the coordinated development of ecological environment and economy.