Reservoir sediment severely impacts water supply in water-scarce regions, making reservoir dredging an urgent global issue. The investment required for deep-water dredging far exceeds that for dry land dredging. Therefore, against the backdrop of the national water network construction, this study focuses on a typical inter-basin water transfer project in Northern China. To increase the proportion of dry land dredging volume and save costs, this study uses compensation reservoirs to replace the emptied reservoir in undertaking water supply tasks as a constraint. Single-objective optimization models for single reservoirs and multi-objective optimization models for reservoir groups are established, using game theory comprehensive subjective and objective weighting methods to select the optimal solution. The following conclusions are drawn from comparing the water supply effects under various emptying sequences: the optimal sequence for emptying reservoirs should be determined through precise quantitative analysis; as the dredging is completed, the water supply tends to stabilize; the satisfaction with the water supply and the variance of the water shortage rate are primarily related to reservoirs with a large inflow and storage capacity; dredging occurs according to the descending order of the storage capacity of reservoirs; and the startup proportion of pump stations shows an increasing trend.