Abstract: To investigate the influence of earthquake duration on the seismic performance of tunnels equipped with damping layers, a spectrum-compatible ground-motion generation method considering duration effects is proposed based on the superposition of wavelet functions. Earthquake duration is widely recognized as one of the key characteristics of earthquakes, in addition to amplitude, frequency content, and energy distribution. Although conventional spectrum-compatible ground motions can generally satisfy the target response spectrum, they often fail to accurately reproduce the temporal characteristics of real earthquakes, particularly earthquake duration. Since prolonged seismic excitation may result in cumulative damage, stiffness degradation, and increased structural deformation, incorporating duration effects into the generation of artificial ground motions is essential for a more realistic assessment of tunnel seismic performance. To evaluate the applicability of the proposed approach, a finite-element model of a representative tunnel was established. Dynamic analyses were performed under two structural configurations, namely, tunnels with and without damping layers. The numerical model was subjected to a series of spectrum-compatible ground motions with different durations generated using the proposed wavelet-based method. The tunnel model incorporated the essential characteristics of the surrounding ground, the lining structure, and the damping layers to realistically capture the soil–structure interaction during seismic loading. By comparing the dynamic responses of tunnels with and without damping layers under various earthquake durations, the influence of seismic duration on deformation, stress, and structural damage was systematically evaluated. Using the proposed spectrum-compatible ground-motion generation method, five groups of artificial earthquake records with different durations were generated while maintaining consistency with the same target response spectrum. This ensured that the effects of duration could be isolated without introducing additional uncertainty associated with differences in spectral characteristics. Subsequently, dynamic response analyses were carried out for both tunnel configurations under each set of seismic records. The obtained results were analyzed in terms of deformation response, stress response, and damage evolution to quantify the influence of earthquake duration and to evaluate the effectiveness of the damping layer under different seismic motions. The results demonstrate that the proposed wavelet-based method is capable of generating spectrum-compatible ground motions with very small fitting errors and excellent agreement with the target response spectrum. Compared with conventional artificial ground-motion generation methods, the proposed approach effectively preserves both spectral compatibility and prescribed duration characteristics, thereby providing a reliable basis for investigating duration-dependent seismic behavior. The generated ground motions not only satisfy the required spectral constraints but also exhibit realistic temporal evolution, making them suitable for dynamic analyses in earthquake engineering applications. The numerical simulation results further indicate that earthquake duration has a significant influence on the seismic response of tunnels. As the duration of seismic excitation increases, the deformation response, stress response, and structural damage of both tunnels with and without damping layers exhibit consistent increasing trends. Longer-duration earthquakes introduce greater cumulative seismic energy into the tunnel, leading to more severe structural responses and higher damage levels. Moreover, the response results under long-duration ground motions show considerably greater variability and dispersion than those obtained under short-duration earthquakes, indicating that seismic duration not only amplifies structural responses but also increases the uncertainty associated with structural performance. A comparison between tunnels with and without damping layers reveals that earthquake duration has a more pronounced influence on deformation and damage than on stress response when damping layers are installed. Under seismic excitations with different durations, the deformation response and damage of the damping tunnel increase significantly with increasing earthquake duration, whereas the corresponding increase in stress response is relatively limited. Specifically, under the longest-duration earthquake considered in this study, the maximum deformation response of the tunnel with damping layers is 66.88% greater than that under the shortest-duration earthquake. Similarly, the corresponding damage level increases by more than 50%, demonstrating the substantial cumulative effect of prolonged seismic loading on structural deterioration. In contrast, the stress response increases by only 10.12%, suggesting that earthquake duration has a comparatively minor influence on stress development. These findings indicate that the differences between long- and short-duration earthquakes are much more evident in terms of deformation and damage than in terms of stress response, regardless of whether the tunnel is equipped with damping layers. The study demonstrates that earthquake duration should be regarded as an important parameter in the seismic assessment and design of underground structures. Ignoring duration effects may lead to an underestimation of structural deformation and damage, particularly for tunnels subjected to long-duration earthquakes. The proposed spectrum-compatible ground-motion generation method provides an efficient and reliable tool for producing artificial seismic records that simultaneously satisfy target spectral characteristics and prescribed duration requirements. Furthermore, the numerical results highlight the necessity of considering earthquake duration in evaluating the seismic performance of tunnels with and without damping layers. The findings of this study provide practical guidance for tunnel seismic analysis and design considering earthquake duration effects and contribute to improving the seismic resilience and safety of underground transportation infrastructure subjected to complex seismic hazards.