The overlying strata layers of coal workfaces with karst aquifer water normally causes serious safety problems due to the precipitation, drainage and water inrush, such as a wide range and long term of surface subsidence. In this study, by taking 10,301 working faces of the Daojiao coal mine in Guizhou Province as the engineering background, the numerical model of water-bearing strata with fluid-solid coupling was established by using UDEC to illustrate the laws of overlying strata movement and surface subsidence. A theory model was proposed to calculate the surface settlement caused by the drainage of aquifer based on the principle of effective stress modified by the Biot coefficient αb. The results showed that the corresponding maximum value (0.72 m) and the range of the surface subsidence with the occurrence of karst aquifer water were larger than that of the overlying strata without karst aquifer water (e.g., the maximum value of surface subsidence with 0.1 m). Moreover, the surface subsidence caused by the drainage of aquifer accounted for 17.8% of the total surface subsidence caused by coal mining. According to the field monitoring of surface subsidence in 10,301 working faces, the maximum value was 0.74 m, which was highly consistent with the results of numerical simulation and theoretical analysis. It verified the accuracy and reliability of the numerical model and the theory model in this study.