Based on coal mining above aquifers of Carboniferous limestone in a coal mine in North China Mining Area, the numerical method of CDEM (Continuum-based Discrete Element Method) was employed to simulate the movement of overburden stratum and damage evolution of floor stratum during coal mining above aquifers. The results indicated that the lithology, thickness, and structure of the impermeable strata and the pressure of confined water were the most pivotal elements which lead to the risk of water inrushes and damage evolution of floor stratum. In addition, the activities of overburden stratum, such as deformation, stratum separation, caving, also exhibited important effects. Compared to caving activities of the immediate roof and main roof, the critical upper strata with the larger thickness and strength showed more important influence on the damage evolution of floor stratum and water inrush risk, although it was relatively far from the coal seam. Before the initial caving of critical roof, the destruction extent of floor stratum and the risk of water inrush increased with the increase of the mined-out area and reached their peaks when the maximum caving interval was reached. When critical strata started periodic caving, the extent of destruction of floor and the risk of water inrush reached their peaks when hanging arch of critical strata reached the maximum value in this period. For caving interval in critical strata is larger than the mail roof and the stress pressure was mainly applied in the rear of the mined-out area other than the mining face, it is difficult to observe the rules of the activities of critical strata above coal seam through conventional mining monitoring ways. The activities of critical strata above coal seam should be studied to effectively prevent water inrush disaster in coal mine.