<p>Tunnel-slope systems in western China are key components of transportation infrastructure, and their long-term stability is threatened by the combined effects of earthquakes and rainfall. Seepage–dynamic coupled simulations were conducted through the secondary development of FLAC^3D. Based on an actual engineering project in western China and the related shaking table test, corresponding numerical models were established to investigate the dynamic response and failure mechanisms of the tunnel–slope system under rainfall–seismic coupling. Results show that rainfall significantly modifies seismic wave propagation and amplifies the overall dynamic response, with peak acceleration increasing by up to 47.4%. Analyses in the frequency and time-frequency domains indicate that this amplification mainly stems from the enhancement of frequency components above 3 Hz under rainfall. Furthermore, tunnel intensifies this high-frequency amplification, leading to a more dispersed distribution of seismic wave energy of slope. Rainfall increases the slope’s sliding risk by weakening the weak interlayer and promoting shear deformation, while the tunnel shifts the main deformation and potential sliding area upward above the tunnel. These findings provide insight into the dynamic stability evaluation of similar tunnel–slope systems.</p>