Under the background of a large reduction in the sediment into the Three Gorges Reservoir (TGR), dispatching of medium-and-small-scale flood in flood season has exacerbated the risks of sediment deposition and flood control in TGR and reduced the chances of large discharge of the reservoir. Studying the dynamic dispatching of “storing clear water and releasing muddy water” in flood season is conducive to further optimizing the dispatching mode. Using one-dimensional unsteady flow mathematical model of the mainstream and tributaries of TGR, we put forward the dynamic operation scheme of “storing clear water and releasing muddy water” in flood season of TGR through calculations. The calculation results illustrate that the dynamic operation mode of “storing clear water and releasing muddy water” in flood season takes into account both sediment discharge, power generation and flood control. A water level at 150 m when “storing clear water” is superior to 155 m; the water level can fluctuate between 145 m and 150 m in the period of “storing clear water”. We recommend to start the releasing of muddy water when the sediment concentration of Cuntan station reaches 2.0 kg/m³ and meanwhile the incoming flow of Cuntan station on that day exceeds 25 000 m³/s; on the contrary, when the sediment concentration of Cuntan station falls to about 0.1 kg/m³ , we suggest to end the releasing of muddy water and begin to store clear water. The research findings provide reference for the optimal operation of TGR in flood season.