The influx of roof water from exceptionally thick sandstone aquifers in northwestern China’s mining regions presents considerable challenges to the safety and productivity of coal mining operations. However, a significant gap in the literature persists concerning the underlying mechanisms. In this study, we investigated coal-seam mining beneath the exceptionally thick sandstone aquifer of the Zhiluo Formation at the Lingxin Coal Mine, utilizing this context as the basis for our engineering analysis. Our examination probed the hydrogeological and geomechanical mechanisms responsible for the abrupt alterations in overburden fractures and their catastrophic consequences during close-seam mining operations, employing research methodologies such as a theoretical analysis, fluid–structure-coupled simulation, and comparative evaluation. The study highlighted the intricate interplay between compressive-shear loads and the mechanics of hydraulic fracturing processes. The results revealed that in the absence of waterproof coal pillars, the downward mining of the L1614, L1615, and L1616 working faces led to the overlying rock’s water-conducting fractures reaching 204.9 m. This height was equivalent to 20 times the combined mining thickness of the three coal seams, impacting both the K3 and K4 aquifers. Conversely, when the water-resistant coal pillars were retained during the downward mining of the L1814, L1815, and L1816 working faces, the maximum height of the water-conducting fractures in the overlying rock was 103.5 m. This height was 10 times the combined mining thickness of the three coal seams, affecting only the K4 aquifer. Notably, vertical hydraulic fracturing was observed when the water pressure variation in the K3 aquifer exceeded 2–3 times its initial value. The water-conducting fracture zone was primarily characterized by the presence of “Type I-II” fractures, with the termination point of each fracture influenced by pressure and shear forces. Furthermore, we established a “fracture cracking and propagation model” and a “hydraulic fracturing-induced disaster model” based on the principles of fracture mechanics. We also provided formulas for calculating the cracking angles and extension heights of overburden fractures’ endpoints, which were derived from the maximum normal stress criterion.