The long-term operation of the reservoir at the flood limit water level in the flood season is not conducive to the exertion of the comprehensive benefits of the reservoir, especially in the flood free period, the operation of the reservoir at the flood limit water level will cause a certain waste of resources. On the one hand, with the continuous improvement of the forecast accuracy, the effective forecast period of flood forecast will continue to extend, when there is excess water in the flood free period, the water level can be raised instead of abandoning the water to increase the benefit of power generation. If there is a flood, it can be discharged within the effective forecast period of flood forecast to make the water level drop back to the flood limit level, so as to ensure the safety of flood control; On the other hand, affected by the forecast uncertainty and other factors, the higher the operating water level in the flood free period, the greater the risk that the water level can return to the flood limit water level through discharge, and the decision-making based only on the power generation benefit and risk rate is difficult to deal with the possible large-scale flood events in the future. This study proposes a dynamic water level decision-making system in flood free period. The system considers three factors: power generation benefit, discharge in the effective forecast period of flood forecast and risk rate. It can provide decision-makers with a variety of decision-making schemes and screen the optimal scheme, thus improving the operational benefit of hydropower station in flood season and reducing flood control risk. Firstly, historical data and various flood season staging methods are used to divide the flood season into multiple sub-seasons, and then the maximum inflow process in the effective forecast period of flood forecast in each sub-season is selected. According to this inflow process, the upper limit of operating water level in the flood free period of each sub-season is determined based on the reservoir discharge capacity, and the operating water level points and discharge ratio are discretized, Then the multi-order Monte Carlo Markov chain (MCMC) and Monte Carlo method are used to calculate the risk rate. Then, the scheme set is established by the three variables of power generation benefit, discharge ratio and risk rate. Finally, the weighted Topsis method is used to determine the optimal scheme. In the practical application, the influence of each risk factor on the risk rate and the influence of weight on the final decision are also compared and analyzed. This method has been verified in Youjiang reservoir in Yujiang River Basin. The main conclusions are as follows: (1) Combined with the discharge in the forecast period, the reservoir operating water level has a certain lifting space in the flood free period, which can effectively reduce the waste of resources. (2) In the discharge process in the forecast period, runoff forecast error and discharge error are the two factors that have the greatest impact on the risk rate, and the multi-order MCMC method effectively reflects the relationship between the adjacent periods of runoff forecast error, and its simulation process is closer to the reality. (3) Topsis with the combination of AHP and entropy weight method can fully consider the characteristics of power generation benefit, discharge ratio and risk rate, and it is effective to select the optimal solution from the set of non-inferior schemes. This method provides a new idea for determining the operating water level of the reservoir in the flood season.