Abstract: Natural and artificial underground cavities exhibit complex geometries, and their influence on the spectral composition of ground motion at sites remains unclear. Based on a parametric characterization framework for irregular cavity geometry, this paper constructs a comprehensive shape parameter (CSP) through principal component analysis. Using finite element numerical simulations, the modulation effects of irregular cavities on the surface Fourier spectral ratio are systematically examined under varying ground motion amplitudes. The results indicate that the presence of irregular cavities induces a spectral modulation featuring low-frequency amplification and high-frequency suppression, and this effect becomes more pronounced as cavity irregularity increases. As the input ground motion amplitude increases from 0.10 g to 0.50 g, the spectral amplification factor exhibits a non-monotonic trend, increasing then decreasing; however, the correlation between CSP and spectral ratio weakens progressively, suggesting that soil nonlinearity under strong earthquakes progressively overshadows the influence of cavity geometry. This study may serve as a reference for seismic fortification of sites containing irregular cavities.