The multiple uncertainties of soil properties and ground motions significantly affect the seismic response of high concrete face rockfill dams (CFRDs). Three types of randomness (the material parameter randomness, stochastic seismic excitation, and their coupling) are generated by stochastic ground motion model and generalized F-discrepancy (GF-discrepancy) method. The generalized probability density evolution method (GPDEM) is used to analyze the influence of randomness on the stochastic dynamic response and system reliability of high CFRDs. The limit state of CFRD is defined according to the crest subsidence and the stress of face-slab, and a performance-based reliability evaluation framework is established. The results show that the randomness of ground motions dominates stochastic dynamic response of the CFRD and the dynamic reliability at different safety thresholds can be obtained by the above methods. Moreover, the proposed seismic safety evaluation framework provides a significant guidance for designing and analyzing practical engineering projects.