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Runoff is an important basis for the operation of hydropower. However, due to inflow uncertainty, the ideal practical operation process usually doesn't match with the plan, which exacerbates the power generation and ecological risks. Therefore, the purpose of this paper is to investigate the relationship between hydropower generation, ecology and their risks under the uncertainty of inflow. Gibbs sampling based on the copula function is presented to simulate the runoff. The scenario tree method is employed to describe the inflow uncertainty. The power generation risk operation model is developed based on the Mean-variance method. In addition, the expected minimum ecological risk model and its comparison model are proposed to analyze the relationship between power generation and ecological risk. The proposed methods are applied to a case study of the Lancang River cascade hydropower station. The results show that (1) The power generation risk of risk operation model decreased by 86.41% at the 90% scenario reduction level, compared with deterministic model. (2) There is an obvious competitive relationship between ecology and power generation, in the case of a 1% loss of expected power generation, the expected ecological risk can be reduced by 6.14%. • The Gibbs sampling model based on copula function is presented to simulate runoff. • The scenario tree method is employed to describe the uncertainty of inflow. • The Mean-variance is introduced to build the reservoir risk operation model. • The trade-off between hydropower generation, ecology and their risks of cascade hydropower stations is analyzed. [ABSTRACT FROM AUTHOR]