To fill the gap that the impact of segmental joints and water-saturated soil is commonly considered separately in the existing research, this paper proposes a fluid-solid coupling FEM to examine the seismic behaviour of an underwater segmented tunnel, considering the weakening effect of the joints and the dynamic characteristics of the two-phase media simultaneously, with different input ground motions, buried depth, and soil stiffness. The presence of segmental joints leads to an increase of pore water pressure in the surrounding saturated soil of the tunnel, implying a greater probability of liquefaction. It also leads to an increase in the tunnel deformation due to a reduction of stiffness. Furthermore, although it beneficially decreases the overall lining forces, it is found to significantly increase the compressive stress at the lining edges near the segmental joints, inducing stress concentration accordingly. Finally, the compressive stress of the tunnel lining and pore water pressure of saturated soil have the most and the least sensitivity to the weakening effect of joints, respectively.