In order to further improve the safety and stability of tunnel structures in high-intensity fractured-zone strata during earthquake, compressive strength test, splitting tensile strength test and scanning electron microscopy (SEM) test were conducted on concrete specimens prepared with different modified materials in this study. The effects of NaOH concentration, fiber content and metakaolin content on the failure mode and mechanical properties of rubber concrete were investigated. The improvement mechanism of these parameters on the mechanical properties of rubber concrete was analyzed from a mesoscopic perspective. Based on the active fault zone of the Shantou Bay Tunnel project, a dynamic model of a fault-crossing tunnel with a rubber concrete structure was established. The mechanical response characteristics of the tunnel lining structure were analyzed. The results show that: (1) The most significant improvement in specimen strength is achieved by owing to its physical filling and pozzolanic effects. When the metakaolin content is 15%, the compressive strength and splitting tensile strength of the modified concrete are increased by 65.3% and 91.1% respectively. (2) The strength of the concrete specimens first increases and then decreases with the increase in fiber content. The peak value occurs when the PE fiber content is 2% by volume, and the strength is increased by 15.9%. (3) The NaOH concentration improves the specimen strength to a certain extent, but its effect is relatively limited. (4) Obvious abrupt changes are observed in the maximum principal stress of the lining near the fault. The main affected area is concentrated within 20 m on both sides of the fault. This section should be regarded as the key area for seismic mitigation. (5) With the increase in ductile layer thickness, the displacement peaks are reduced by 15.42%, 27.96%, and 31.39%, respectively. Considering both seismic mitigation performance and engineering economy, it is reasonable to set the ductile layer thickness at 15 cm. The modified rubber concrete developed in this study provides a reference for enhancing the resilience of fault-crossing tunnels.