Hydraulic tunnels are prone to pass through faults and high-intensity earthquake areas, which will cause serious damage under fault dislocation and earthquake action. Fault dislocation and seismic excitation are often considered separately in previous studies. For tectonic earthquakes with higher frequency in seismic phenomena, fault dislocation and ground motion are often associated, and fault dislocation is usually the cause of earthquake occurrence, so it is limiting to consider the two separately. Moreover, strong earthquake records show that there will be significant differences in the mainland vibration within 50 m. The uniform ground motion inputs in previous studies are not suitable for long hydraulic tunnels. This paper begins with the simulation of non-uniform stochastic seismic excitations that consider spatial correlation. Based on stochastic vibration theory, multiple multi-point acceleration time-history curves that can reflect traveling wave effects, coherence effects, attenuation effects, and non-stationary characteristics are synthesized. Furthermore, a fault velocity function is introduced to account for the velocity effect of fault dislocation. Finally, numerical analyses of the response patterns of the tunnel lining under four different conditions are conducted based on an actual engineering project. The results indicate the following: (a) the maximum lining response values occur under the combined effects of fault dislocation and non-uniform seismic excitation, indicating its importance in the seismic resistance of the tunnel. (b) Compared to uniform seismic excitation, the peak displacement of the tunnel under non-uniform seismic excitation increases by up to 6.42%, and the peak maximum principal stress increases by up to 28%. Additionally, longer tunnels exhibit a noticeable delay effect in axial deformation during an earthquake. (c) Under non-uniform seismic excitation, the larger the fault dislocation magnitude, the greater the peak displacement and peak maximum principal stress at the monitoring points of the lining. The simulation results show that the extreme response values primarily occur at the crown and haunches of the tunnel, which require special attention. The research can provide valuable references for the seismic design of cross-fault tunnels.