Ion erosion has a significant impact on the long-term service performance of lining structures in the subsea tunnel and seriously affects its sustainability. Indoor tests are usually used to study the erosion behavior of lining concrete specimens to reveal the degradation pattern of ion erosion. However, the long-term service performance of lining structures under ion erosion is rarely considered in the industry. In this study, the long-term deterioration characteristics of concrete specimens and subsea tunnel linings are analyzed by using numerical investigations. The long-term diffusion patterns of erosion ions in concrete specimens are evaluated. The effects of ion erosion and water pressure on the stress, deformation, and damage characteristics of the lining structure are examined. The numerical results show that solution concentrations and concrete grades have a significant influence on the ion diffusion in concrete specimens. As the erosion time increases, the rate of ion diffusion gradually decreases due to the decrease in the concentration difference between the inside and outside of the concrete. The service time T has a significant effect on the depth and rate of ion erosion. When T is 10, 50, and 100 years, the depth of ion erosion reaches 25, 63, and 84 mm, respectively, showing a nonlinear increase. As the depth of ion erosion increases, the characteristic parameters reflecting the long-term performance of the lining structure will increase. The maximum tensile stress is 0.98 MPa, and the maximum displacement is 1.59 cm, both of which occur at the arch crown. Disregarding the effects of ion erosion and water pressure, the vertical displacements of the lining structure within the first two years under low loads account for more than 97% of the 100-year displacements. Both ion erosion and water pressure exacerbate the damage deterioration of the lining, in which ion erosion significantly increases the maximum tensile stress of the lining, with a maximum enhancement of 326.09%, and water pressure significantly enlarges the maximum compressive stress of the lining, with a maximum enhancement of 53.23%. However, with increasing depths of ion erosion, the high water pressure will reduce the maximum tensile stress. This study can lay the foundation for further research on the long-term stability of the lining under complex erosion environments.