This paper considers a fully coupled 3D BEM-FEM analysis for the ship structural hydroelasticity problem in waves. Fluid flows and structural responses are analyzed by using a 3D Rankine panel method and a 3D finite element method, respectively. The two methods are fully coupled in the time domain using a fixed-point iteration scheme, and a relaxation scheme is applied for improve convergence. In order to validate the developed method, numerical tests are carried out for a barge model. The computed natural frequency, motion responses, and time histories of stress are compared with the results of the beam-based hydroelasticity program, WISH-FLEX, which was thoroughly validated in previous studies. This study extends to a real-ship application, particularly the springing analysis for a 6500 TEU containership. Based on this study, it is found that the present method provides reliable solutions to the ship hydroelasticity problems.