Abstract: To effectively mitigate multiple water disaster risks—including water from thick unconsolidated layers and floor limestone aquifers—confronted during deep mining operations in the Huainan Coalfield, this study targets the Huainan Coalfield as the research object. Leveraging literature review, field investigation, and data analysis, a comprehensive evaluation model integrating qualitative description and quantitative calculation is constructed to conduct hierarchical assessment of mine hydrogeological types. Based on the assessment outcomes, a multi-element synergistic linkage model for coal mine water disaster prevention and control is established by integrating floor limestone ground regional treatment technology, roof water precise drainage and blocking technology, and aboveground-underground three-dimensional prevention and control strategies, followed by engineering verification through typical cases. The results indicate that the average score of the Huainan Coalfield’s hydrogeological type after comprehensive evaluation is 3.25, and the water disaster development in this region presents an evolutionary characteristic of “complex-extremely complex”, whose formation and evolution process are governed by the coupling effect of multi-water-source interactive recharge and multi-channel linkage penetration. Engineering application effects show that by adopting the multi-element water disaster prevention and control model, the floor water inrush coefficient of the working face in Zhangji Coal Mine is successfully reduced to 0.016 6 MPa/m, realizing effective water disaster management and ensuring the safe production of the mine. The study suggests that this multi-element prevention and control model achieves the transformation from “local passive treatment” to “global active pre-control”, providing a scientific theoretical reference and technical path for the precise prevention and control of water disasters in the Huainan Coalfield and mines under similar geological conditions.