Abstract: The groundwater flow and solute transport mathematical model was established based on FEMWATER module of GMS software according to the hydrogeological condition in Lai’an county, Chuzhou. The trend of migration and the environmental impact of COD_Cr and BOD in groundwater are predicted and evaluated under the abnormal working conditions in an animal protein production site. The results of numerical simulation show that the maximum migration of COD_Cr and BOD are 110 m and 135 m after 30 days in production area respectively, and the corresponding concentration are 1800 mg/L and 770 mg/L. In addition, the migration of COD_Cr and BOD are longer with high concentration under the absence of seepage prevention measures which resulting in a significance impact to the quality of phreatic water.