During flood control reservoir operation, uncertainties in inflow forecast, the reservoir discharge capacity curve, and the reservoir storage curve significantly impact the reservoir operation processes and cause flood risk. This article proposes an improved stochastic differential equation (SDE) method for flood-risk analysis. The uncertainties mentioned above were quantified, and the mean and variance of the water level at each time step were calculated, then the flood risk was estimated and the impact of these uncertainties on flood control reservoir operation was evaluated. The Three Gorges Reservoir (TGR) was selected as a case study. Results show that the variance of the water level at each time step does not monotonically increase over time. Inflow forecast and flood hydrograph shape work together and have a great influence on the flood risk. The method provides a way for flood-risk assessment for flood control reservoir operation.flood control reservoir operation, flood-risk analysis, stochastic differential equation, Three Gorges Reservoir, uncertainties