The Huanglong Coalfield in the southern Ordos Basin is widely threatened by bed-separation water hazards. Under conditions of ultra-thick coal seam mining and a weak argillaceous aquiclude, the separation and fracture development in conglomerate strata are challenging to accurately characterize. To evaluate the bed-separation characteristics in conglomerate strata during ultra-thick coal seam mining, this study focuses on the water inrush accident at the Guojiahe Coal Mine. Through mechanical property analysis of overlying strata, mechanical analysis of key layers, and aquifer water level monitoring, the locations of bed separations in the overlying strata were determined. A 3D geological model was established using 3DEC to simulate overlying strata failure and conglomerate fracturing. The results indicate that: (1) The roof conglomerate in the study area is weakly cemented and prone to fracturing under high-intensity disturbance from fully mechanized top-coal caving mining, leading to increased porosity, permeability, and water abundance, which can serve as effective water storage spaces; (2) Bed separations are located beneath the Yijun Formation conglomerate; (3) Fractured conglomerate connects with the “cavity"-type bed separation formed below, creating a composite “fracture-cavity” bed-separation structure. This study summarizes the developmental features of conglomerate bed separations, providing engineering insights for the prevention and control of bed-separation water hazards.