Due to the properties of rock strata, uneven subsidence of overlying rocks was induced by coal seam mining. Interlayer separation was easily formed between hard rocks and soft rocks. The space of separation layers was altered during repeated mining of adjacent coal seams, and water inrush disasters from sealed separation layers were likely to occur after water accumulation in such layers. The failure characteristics of roof overlying rocks were investigated, the development height of water flowing fractured zones under repeated mining was determined, and then the strata positions of sealed separation layers in the roof after mining were identified. With the UDEC simulation software, the development characteristics of sealed separation layers were analyzed. By adopting the control variable method, the influences of coal mining height, coal seam interval and thickness of mudstone below sealed separation layers on separation layer development were studied within the mine field. The strata positions of disaster-prone separation layers were confirmed. Further researches revealed that under repeated mining, the space of sealed separation layers was enlarged with the increase of coal mining height, reduced with the increase of coal seam interval, and decreased with the increase of the thickness of underlying mudstone.