The interaction of mining and the surface water or aquifer system in varying overburden strata conditions is one of the most critical aspects of sustainable mining practices, that can lead to water loss or water inrush into openings. This paper examined this phenomenon in a complex strata condition via a case study, and proposed a new mining design to minimize the impact of longwall mining on the overlaying aquifer. A range of factors have been identified contributing to the potential disturbance of the aquifer, including the extent of the water-rich area, the characteristics of overburden rock units, and the development height of the water-conducting fracture zone. In this study, the transient electromagnetic method and the high-density three-dimensional electrical method were used to identify two areas prone to water inrush danger in the working face. The vertical range of the water-rich abnormal area 1 is 45–60 m away from the roof, with an area of 3334 m2. The vertical range of the water-rich abnormal area 2 is 30–60 m away from the roof, with an area of approximately 2913 m2. The bedrock drilling method was used to determine that the thinnest part of the bedrock, with a thickness of approximately 60 m, and the thickest part, with a thickness of approximately 180 m. The maximum mining-induced height of the fracture zone was 42.64 m using empirical method, theoretical prediction based on the rock stratum group, field monitoring. In summary, the high risk area was determined, and the analysis shows that the size of the water prevention) pillar was 52.6 m, which was smaller than the safe water prevention pillar actually set in the mining range. The research conclusion provides important safety guidance significance for the mining of similar mines.