<p>Interconnected cave–fracture networks are widely developed in karst regions. The complex geometric characteristics and strong heterogeneity of these formations not only disturb groundwater flow fields but also alter the in-situ stress state of the surrounding rock, leading to the formation of irregular preferential seepage pathways. These factors pose significant challenges to the long-term stability and construction safety of underground tunnels. In this study, a hydro-mechanical (HM) coupled model is established using COMSOL Multiphysics to investigate the seepage behavior of tunnels under different geological conditions, considering the synergistic effects of cave–fracture systems. The model is validated against classical consolidation problems and fracture seepage cases, and the results show good agreement with analytical solutions and previous studies, indicating its reliability. The results show that increasing fracture density enhances network connectivity, resulting in higher seepage pressure on the tunnel lining accompanied by greater non-uniformity. In addition, larger cave radius, shorter cave distance, and higher cave pressure further increase the seepage pressure on the lining, with caves located above the tunnel exerting a more pronounced influence on the upper section. When a connected seepage pathway forms between the cave, fractures, and lining, the local seepage pressure is more likely to exceed the lining bearing capacity. These findings suggest that targeted anti-seepage measures, such as grouting reinforcement, are necessary in high-risk zones, and provide a basis for the adaptive design of tunnel linings in karst regions.</p>