Climate change has resulted in an increase in extreme weather events, with a sharp rise in droughts and floods. To establish a long-term mechanism for ensuring the safe operation of the Three Gorges Project, it is imperative to utilize hydrodynamic methods to analyze the water level operation mode during the flood season. This is crucial to enhancing the flood control safety and maximizing the overall benefits of this project. Therefore, this study obtained four different frequency design flood processes for each year by utilizing data from typical years. And the influence of different starting water level and discharge flows on the high water level and excess flood volume of flood regulation were revealed under the existing scheduling protocols and a one-dimensional hydrodynamic model. The results indicated that the water level operation modes of floods from different typical years were significantly different under the same scheduling rules, and when faced with the extreme flood conditions, discharge flow is a primary determinant of reservoir safety. Furthermore, the current scheduling scheme for the Three Gorges Reservoir has an extra safety margin. As a result, even without forecasting inflows, elevating the operating water level to 155 m during the flood season effectively mitigates risks from floods with a return period of 100 years or less, while maintaining risk control over floods with 1,000-year or 10,000-year return periods.