To investigate the seismic response of layered rock sites, a multidomain analysis method was proposed. Three finite element models with infinite element boundaries for layered sites were analysed. The results of this multidomain analysis show that stratum properties and elevation have an impact on wave propagation characteristics and the dynamic response of layered sites. Compared with the rock mass, the overlying gravel soil has a greater dynamic amplification effect at the sites. A time domain analysis parameter PGA(IMF) was proposed to analyse the effects of different strata on the seismic magnification effect of layered sites, and its application was also discussed in comparison with PGA. According to the frequency domain analysis, the interface of the rock mass strata has a low impact on the Fourier spectrum characteristics of the sites, but gravel soil has a great magnification effect on the spectrum amplitude in the high-frequency band (≥30 Hz) of waves. Moreover, the stratum properties have a great influence on the shape and peak value of the Hilbert energy and marginal spectrum at layered sites. When waves propagate from hard rock to soft rock, the peak value of the Hilbert energy spectrum changes from single to multiple peaks; then, in gravelly soil, the Hilbert energy spectral peak, its nearby amplitude and the amplitude in the high-frequency band (28–36 Hz) are obviously amplified. The frequency components and amplitude of the marginal spectrum become more abundant and larger from rock to gravelly soil in the high-frequency band (28–35 Hz).