Drainage to lower water pressure is an effective measure for preventing and controlling water ingress when mining above a confined aquifer. The deep limestone aquifer in the Huaibei mining area, China, generally has high pressure, low permeability and variable water abundance, so it is difficult to meet single-borehole drainage requirements. In order to achieve good drainage, and take into account engineering and environmental protection requirements, a multi-objective optimization model of group borehole drainage was established. The model takes the minimization of single-hole flow and borehole numbers as the objective functions, and the drawdown in drainage boreholes and the water level control point as the constraint conditions. The particle swarm optimization algorithm was used to solve the model. The results indicate that, for a low permeability aquifer, measures such as using partially penetrating wells, increasing the number of drainage boreholes appropriately and reducing individual borehole yield have good drainage effects. The extent of drilling and amount of drainage are also relatively small. This is all to the good for the drainage. When the optimization results were applied to coal-face drainage in Huaibei the outcome was good.