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Although intensive research of the influence of ground motion duration on structural cumulative damage has been carried out, the influence of dynamic responses in underground tunnels remains a heated debate. This study attempts to highlight the importance of the ground motion duration effect on hydraulic tunnels subjected to deep-focus earthquakes. In the study, a set of 18 recorded accelerograms with a wide-range of durations were employed. A spectrally equivalent method serves to distinguish the effect of duration from other ground motion features, and then the seismic input model was simulated using SV-wave excitation based on a viscous-spring boundary, which was verified by the time-domain waves analysis method. The nonlinear analysis results demonstrate that the risk of collapse of the hydraulic tunnel is higher under long-duration ground motion than that of short-duration ground motion of the same seismic intensity. In a low intensity earthquake, the ground motion duration has little effect on the damage energy consumption of a hydraulic tunnel lining, but in a high intensity earthquake, dissipation of the damage energy and damage index of concrete shows a nonlinear growth trend accompanied by the increase of ground motion duration, which has a great influence on the deformation and stress of hydraulic tunnels, and correlation analysis shows that the correlation coefficient is greater than 0.8. Therefore, the duration of ground motion should be taken into consideration except for its intensity and frequency content in the design of hydraulic tunnel, and evaluation of seismic risk.