In order to consider the time-dependent characteristic of risk factors of hydropower project, the method of stochastic process simulating structure resistance and load effect is adopted. On the basis of analyzing the structure characteristics and mode of operation, the operation safety risk rate assessment model of hydropower project is established on the comprehensive application of the improved analytic hierarchy process, the time-dependent reliability theory and the risk rate threshold. A scheme to demonstrate the time-dependent risk rate assessment method for an example of the earth-rock dam is particularly implemented by the proposed approach. The example shows that operation safety risk rate is closely related to both the service period and design standard; considering the effect of time-dependent, the risk rate increases with time and the intersection of them reflects the technical service life of structures. It could provide scientific basis for the operation safety and risk decision of the hydropower project by predicting the trend of risk rate via this model.