The mechanical behaviour of a rectangular tunnel structure equipped with flexible joints under normal fault displacement, together with the failure characteristics of the overlying soil, was investigated in this study. To this end, a series of quasi-static model tests with an approximate geometric similarity ratio of 1∶30 was conducted. A rectangular tunnel crossing a 60° normal fault was adopted as the research object. The displacement response, strain distribution, and soil–structure contact pressure of the tunnel were systematically analysed. In addition, the lining failure process and the evolution of surface ground deformation and cracking were comprehensively monitored. The test results indicate that the flexible joints can effectively absorb and distribute the displacement and energy input caused by fault displacement, thereby reducing the overall damage to the tunnel structure. In accordance with standard fault displacement conditions, distinct cracks were observed to form on the ground surface, and significant step-off and sand leakage were recorded between segments E and F. This observation indicates that fault displacement was predominantly concentrated at the structural joints. The stress distribution in the tunnel structure exhibits distinct asymmetrical characteristics: the roof of the upper bench and the floor of the lower bench are subjected primarily to longitudinal tension, while the floor of the upper bench and the roof of the lower bench are subjected primarily to longitudinal compression. In localized areas, this process is accompanied by crack propagation, surface spalling, and block detachment. Subsequent analysis has revealed that the fault shear zone exhibits a narrow, inverted triangular distribution, with the mechanical response being most evident at the points at which the tunnel intersects this area. Consequently, it is imperative that the fault shear zone and its adjacent sections are designated as key areas for fault-resistant design in underground tunnel projects crossing faults..