The influence of the sealing degree of the lining structure and the permeability of surrounding rock on the stability of the tunnel has always been the main topic concerned by the relevant engineering researchers. Based on the research background of the tunnel project of Qingdao metro line 1 and the in-depth analysis of the existing research results, this paper makes a systematic analysis and research on the influence mechanism of the sealing degree of the lining structure and the permeability of surrounding rock on the stability of the tunnel by the numerical simulation. The results show that the safety coefficient of each part of lining structure decreases with the increasing degree of tunnel sealing, which is manifested by the increase of the settlement of the vault and the convergence of the arch foot. In addition, the stability of surrounding rock becomes worse with the increase of permeability coefficient of surrounding rock, which means the higher pore pressure and larger displacement of rock around the chamber. At the same time, the influence of the sealing degree of the lining structure on the stability of the tunnel will increase with the permeability of the surrounding rock. The works in this paper have guiding significance for the construction of submarine tunnel under different characteristics of surrounding rock and the selection of sealing degree of lining structure.