Real-time flood control operations of a cascade reservoir system under emergency conditions can reduce the social and economic loss caused by natural disasters. This paper proposes a risk-based model for real-time flood control operation of reservoirs under emergency conditions and uncertainties. The proposed model consists of three modules: emergency scenarios establishing, Monte Carlo simulations, and risk analysis. The emergency scenarios considered are earthquakes, extreme floods and failure of the spillways of a reservoir. The uncertainty factor considered is the forecast error of reservoir inflows, arising from model structural uncertainty and parameter estimating. The Monte Carlo simulations conduct the real-time flood control operation of reservoirs considering the proposed emergency events and uncertainties. The module of risk analysis performs the assessment of the operation schedules and calculates the risk of dam overtopping, based on the results from Monte Carlo simulations. The proposed model is applied to a cascade reservoir system in the upper reaches of Daduhe river basin in China. The results show that the maximum initial water level of the Shuangjiangkou reservoir is 2447 m a.s.l. (meters above sea level) using the release capacity model and is 2444.5 m a.s.l. using the command model under the scenario of upstream dam break. The integrated risk of the reservoir increases with the initial water level and the uncertainty degree of the reservoir inflows. The decision-makers can choose the operation models according to the actual initial water level of the reservoir under different emergency scenarios.