The temporal distribution of the flood of the hydropower station can be altered when the upstream hydropower station is constructed synchronously, which may lead to the inapplicability of current diversion risk estimation method.Considering the hydrologic uncertainty of diversion system, a system risk analysis model was established based on risk analysis theory. In view of the correlation between the sectional flood of upper hydropower station and interval-basin flood, the Copula function was used to establish the joint probability distribution, and each flood process was simulated in following by using Monte Carlo method. On this basis, the construction flood of hydropower station was calculated by coupling the simulation of the cofferdam-break flood, routing of river flood and composition of regional flood. Subsequently the system risk was obtained. An engineering case was presented to validate the applicability of the proposed model. And the sensitivity analysis of other risk factors was performed. Additionally, the effect of upper hydropower station on diversion risk was investigated.The study could offer a referential basis for establishment of the diversion standard under the construction of cascade power stations.