In recent years, water inrush from bed separation in coal mines occurs frequently, and the disaster of water inrush in the bed separation is gradually receiving attention. Due to the inrush of bed separation water in overlying strata has characteristics of without obvious precursor and gushing rapidly, it is likely to cause accidents if there is no forecast or handled improperly. Based on the study area of 104 and 106 mining area in Yangliu coal mine of Huaibei Mining Group, the paper determined five main factors that influenced the inrush of water in bed separation by the analysis, then build the geological model to forecast the inrush of water in bed separation by using analytic hierarchy process and modeling capabilities of GIS, and tested the reliability of the model, the results of test are ideal. This research result can directly serve the safe mining of coal seams in the research area and similar mining areas, and also enrich the theory of prevention and control of water inrush from bed separation.