Ocean boundaries present a significant effect on the vibroacoustic characteristics and sound propagation of an elastic structure in practice. In this study, an efficient finite element/wave superposition method (FE/WSM) for predicting the three-dimensional acoustic radiation from an arbitrary-shaped radiator in Pekeris waveguides with a lossy seabed is proposed. The method is based on the FE method (FEM), WSM, and sound propagation models. First, a near-field vibroacoustic model is established by the FEM to obtain vibration information on a radiator surface. Then, the WSM based on the Helmholtz boundary integral is used to predict the far-field acoustic radiation and propagation. Furthermore, the rigorous image source method and complex normal mode are employed to obtain the near- and far-field Green's function (GF), respectively. The former, which is based on the spherical wave decomposition, is adopted to accurately solve the near-field source strength, and the far-field acoustic radiation is calculated by the latter and perturbation theory. The simulations of both models are compared to theoretical wavenumber integration solutions. Finally, numerical experiments on elastic spherical and cylindrical shells in Pekeris waveguides are presented to validate the accuracy and efficiency of the proposed method. The results show that the FE/WSM is adaptable to complex radiators and ocean-acoustic environments, and are easy to implement and computationally efficient in calculating the structural vibration, acoustic radiation, and sound propagation of arbitrarily shaped radiators in practical ocean environments.