Flushing is the most effective way to preserve reservoir storage when a reservoir is completely emptied. However, the efficiency of sediment flushing of empty storage depends on the characteristics of water flow and deposition pattern. In turn, deposition pattern is based on the behavior of sediment transport in a reservoir. In this study, a depth-averaged two-dimensional bed evolution model was applied to simulate the behavior of sediment transport and bed evolution in A-Gong-Dian reservoir during the process of sediment flushing of empty storage. The model boundary conditions for upstream were discharge and suspended sediment concentration hydrographs, and for downstream was water stage. These were simulated by the physiographic soil erosion-deposition (PSED) model. The results of each typhoon event indicated that a significant erosion ditch was generated between Joushui river and a shaft spillway pipe during the process of erosion and deposition due to the flow velocity of empty flushing of the shaft spillway pipe. The phenomenon of erosion and deposition had a large area siltation, narrow and deep gap similar line of erosion. The maximum depth of erosion reached more than a meter, and the phenomenon of re-deposition later. The different efficiency of sediment flushing of empty storage by the shaft spillway pipe for rainfall pattern of each rainfall event, and the average efficiency of empty flushing for the shaft spillway pipe was 62.30%. The simulation results are close to the efficiency obtained from the hydraulic model test in the laboratory which was 65.34%.