Water levels in reservoirs are generally not allowed to exceed the flood-limited water level during the flood season, which means that huge amounts of water spill in order to provide adequate storage for flood prevention and that it is difficult to fill the reservoir fully at the end of year. Early reservoir refill is an effective method for addressing the contradiction between the needs of flood control and of comprehensive utilization. This study selected the Danjiangkou Reservoir, which is the water source for the middle route of the South-North Water Diversion Project (SNWDP) in China, as a case study, and analyzed the necessity and operational feasibility of early reservoir refill. An early reservoir refill model is proposed based on the maximum average storage ratio, optimized by the progressive optimality algorithm, and the optimal scheduling schemes were obtained. Results show that the best time of refill operation for the Danjiangkou Reservoir is September 15, and the upper limit water level during September is 166 m. The proposed early refill scheme, in stages, can increase the annual average storage ratio from 77.51% to 81.99%, and decrease spilled water from 2.439×109 m3 to 1.692×109 m3, in comparison to the original design scheme. The suggested early reservoir refill scheme can be easily operated with significant comprehensive benefits, which may provide a good reference for scheduling decision-making.