Abstract: A substructure analysis method for water-axisymmetric cylinder dynamic interaction problems is presented to simulate the seismic response of water-structure interactions. According to the wave equation and boundary conditions for the three-dimensional incompressible water and by applying the method of separation of variables, the model is transformed into a two-dimensional model, which is analytical in the circumferential direction and numerical in the vertical and radial directions. The dynamic stiffness equation of the infinity water at the truncated boundary is derived by using the scaled boundary finite element method, then the hydrodynamic pressure on the structure can be obtained by coupling the finite element equation of the near field water with the hydrodynamic on the truncated boundary. The finite element equation in time domain of a water-axisymmetric cylinder interaction system is developed by coupling the finite element equation of the structure with the hydrodynamic pressure. The numerical examples demonstrated that the proposed method is accurate and efficient. Numerical results show that the effect of the hydrodynamic pressure on the natural frequency and the dynamic response of the axisymmetric structure is increasing with the increase of the water depth in general.