During the long-term service of water diversion tunnels, the mechanical properties of the surrounding rock and lining materials deteriorate over time due to various physicochemical actions, leading to cumulative internal mesoscopic damage. To evaluate the long-term safety of tunnels, initial mechanical parameters of the surrounding rock are obtained through displacement inversion. Utilizing a creep damage model based on internal variable thermodynamics, which considers material degradation and structural damage of tunnel, the long-term evolution process of tunnel deformation has been simulated. Furthermore, a long-term safety assessment of the tunnel is conducted based on deformation indicators. The results demonstrate that under different conditions of degradation and damage, the time-dependent deformation of tunnels exhibits distinct evolutionary characteristics. When the strength reduction coefficient is no less than 0.7, tunnel deformation follows a pattern of initial increase followed by stabilization. In contrast, when the strength reduction coefficient is below 0.6, tunnel deformation initially increases rapidly, then gradually slows down before accelerating again. As the strength reduction coefficient decreases, the magnitude of tunnel deformation increases, and the onset time for secondary acceleration occurs earlier. Based on these deformation evolution characteristics, a 3S evaluation method for assessing the structural safety factor of tunnels is proposed.