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Mine water disaster is closely related to the geological structure of the mine. A scientific evaluation of the complexity of the minefield structure can greatly contribute to mining safety. In this study, we optimized the fault impact index in the study area and proposed an improved local linear embedding (LLE) algorithm by investigating the Shengquan coal mine. We analyzed the fault formation age and connectivity between faults in the study area, combined with topology theory, and based on previous studies. The mechanical properties of faults and the influence of small faults on the strata can be combined to derive a quantitative evaluation model of the structural complexity of mines. Based on the evaluation model, the study area was divided into a simple structural area, a medium structural area, and a complex structural area. By comparing the location of water inrush points in recent years with the three-dimensional high-density electrical exploration of the 21,304 working face, the effectiveness and rationality of structural complexity zoning were determined.