This paper proposes a frequency wavenumber-finite element hybrid method with kinetic source model for dynamic analysis of pile founded nuclear island from fault to structure. This method benefits from the effective synthesis of broadband ground motions by the fault source model, the realism of frequency wavenumber for earthquake simulation from fault to the site and the mesh refinement capabilities of the finite element in modeling the nuclear structure and the near soil. This method achieves the expression of source rupture, wave propagation, site response, soil-structure interaction, soil nonlinearity and structure response accurately, which solves the multi-scale problem from crustal layer to nuclear structure. Under finite-fault excitation, the correctness of the proposed method is validated by comparing with the frequency wavenumber method. Then, a full process seismic simulation of a pile founded nuclear island built on a non-rock site is conducted. The influence of source parameter and soil-structure interaction is studied. Results indicate that the change of source parameter can lead to difference nuclear island failure direction. With the increase of dip angle, the appearance of maximum stress is in advance. The soil nonlinearity could greatly amplify the soil-structure interaction effect and the loads on piles. The connection between the containment vessel and the raft is vulnerable and the piles on the edge of the raft is prone to damage. This hybrid method could accomplish an appropriate seismic evaluation of the nuclear structures and the conclusions may provide reference for seismic design of nuclear structure.