Based on the domain reduction idea and artificial boundary substructure method, this paper proposes an FK-FEM hybrid approach by integrating the advantages of FK and FEM (i.e., FK can efficiently generate high-frequency three translational motion, while FEM has rich elements types and constitutive models). An advantage of this approach is that it realizes the entire process simulation from point dislocation source to underground structure. Compared with the plane wave field input method, the FK-FEM hybrid approach can reflect the spatial variability of seismic motion and the influence of source and propagation path. This approach can provide an effective solution for seismic analysis of underground structures under scenario of earthquake in regions where strong earthquakes may occur but are not recorded, especially when active faults, crustal, and soil parameters are available. Taking Daikai subway station as an example, the seismic response of the underground structure is simulated after verifying the correctness of the approach and the effects of crustal velocity structure and source parameters on the seismic response of Daikai station are discussed. In this example, the influence of velocity structure on the maximum interlayer displacement angle of underground structure is 96.5% and the change of source parameters can lead to the change of structural failure direction.