In order to improve the accuracy of results of numerical simulation of groundwater in mining areas with complex faults, we conducted a case study in a mining area in Inner Mongolia, where ten inclined faults were intricately distributed. We used the FEFLOW software to simplify the inclined faults as vertical permeable faults, and established a three-dimensional numerical model of groundwater in the mining area with complex faults. Using the model, we predicted the destruction of the overlying aquifers in the mining area after 30 years. The results show that the drawdown of the Permian Shanxi formation aquifer, affected by exploitation, was about 150. 23 m. The drawdown of the Permian Shihezi formation aquifer and the Neogene aquifer was about 23 m, which was because the water level difference intensified, leading to the increase of flow, and there was no steady aquifuge. The quaternary loose rock pore aquifer was not affected due to the integrated and thick clay layer. The study shows that effective generalization of faults is helpful to improve the accuracy of numerical simulation and its results.