<p>Accounting for the nonlinear characteristics of the complex soil-structure interaction, this study conducted numerical simulations of a free-field model and three tunnel-structure models with different flexibility ratios, based on shaking table tests. Based on the validated numerical model, the effects of the flexibility ratio on the seismic response of the frame structure adjacent to the tunnel were analyzed under various seismic inputs. The results indicated that a decrease in the flexibility ratio led to an increase in both the inter-story drift ratio and the top displacement of the frame structure. The differences in the inter-story drift ratio profiles under different seismic intensities became more pronounced as the flexibility ratio decreased. Both a lower flexibility ratio and a higher Peak Ground Acceleration (PGA) amplified the ground surface acceleration response, with the maximum response typically occurring under low-frequency seismic waves. Additionally, a lower flexibility ratio and a higher PGA increased the acceleration response and internal force peaks in the tunnel lining. However, the flexibility ratio did not have a significant effect on the distribution pattern of the tunnel’s internal forces.</p>