To study the hydrochemical characteristics of main aquifers in Jiaojia gold mine area and their changing regularities, exploring the main sources of mine water, 244 water samples from the main aquifers and mine water were collected. The principal components were extracted by factor analysis and shows that with the increase of depth, the concentration of Na+ and Cl− increased significantly, the water–rock interaction becomes stronger, the water quality develops towards salinization, the total water quality, hydrodynamic conditions, and the connection between groundwater and surface water becomes worse. We extracted the main influential discriminant indexes using principal component analysis (PCA), that is, pH, MH4+, NO3−, NO2−, total hardness, TDS, Fe3+, SO42−, Cl− and F−. We weighted the extracted discriminant indexes using entropy weight method (EWM), that is in turn, 0.0002, 0.1883, 0.1272, 0.2061, 0.0680, 0.0613, 0.1461, 0.0573, 0.0844, and 0.0613. 55 water samples from each aquifer in the last 5 years were analyzed by hierarchical cluster analysis (HCA), and the relational degree between the main aquifers and mine water was judged by the distance between them; result shows that the main source of mine water is from the hanging wall of fault aquifer, followed by the footwall of fault aquifer. The mine water has little connection with bedrock weathered fractured aquifer, and almost no connection with Quaternary porous aquifer. The PCA–EWM–HCA model established in this paper provides a theoretical basis for identification of mine water inrush source and protection of underground water resources.