Corrosion of steel bars due to chloride ions in seawater migration into reinforced concrete (RC) lining is a major factor affecting the lifetime of subsea tunnels. To improve the safety assessment of existing subsea tunnels, a hydraulic–mechanical–chemical (H–M–C) coupled model is proposed. The long-term distribution of chloride ions migration process with hydrostatic pressure in the RC lining of subsea tunnels can be simulated more accurately. In the H–M–C coupled model, the volume fluid fraction and convection velocity obtained from the bidirectionally coupled hydraulic and mechanic analysis are unidirectionally considered in the analysis of convection, diffusion, and adsorption of chloride ions in the RC lining. In addition, the classic expression of the effective diffusion coefficient is modified by considering a constrictivity factor that varies nonlinearly with the microscopic pore size. Results indicate that the constrictivity factor has a certain effect on the migration of chloride ions in concrete. The service time of the RC subsea tunnel rapidly decreases as the most frequent gel/capillary pores radius increases on a non-linear curve. If the most frequent gel/capillary pores radius of the concrete is small, by appropriately increasing the thickness of the protective layer, the service time of the RC subsea tunnel can be effectively extended. Conversely, once the most frequent gel/capillary pores radius is large, the service time of the RC subsea tunnel will be greatly shortened. At this time, the increase in the thickness of the protective layer will no longer have significant protective effects. Afterward, the sensitivity analyses are carried out on four sets of parameters i.e., saturated permeability, van Genuchten parameters, initial saturation, and binding capacity parameters. The results of the sensitivity analyses suggest that the effects of the most frequent gel/capillary pores radius on the penetration process of chloride ions in the concrete lining of subsea tunnels are more sensitive to the initial saturation than the van Genuchten parameters. Furthermore, with the increase of the most frequent gel/capillary pores radius, the sensitivity of the chloride ion penetration to capillary pores radius under different chloride binding conditions is increasing.