The so-called large multi-body floating offshore structure is a new type of offshore structure with a huge and extremely flat deck area, which has a promising prospect as a floating port and also in applications in the area of marine space exploitation. Due to its unique structural form, the hydrodynamic and structural response characteristics are very complex. Specifically, due to the instantaneous position variation in the body surface, the nonlinearity of the free surface, the interactions between floating bodies, and the elastic deformation of floating bodies, the nonlinear factors are significant and cannot be neglected. For these kinds of problems, methods based on CFD-FEA (computation fluid dynamics–finite element analysis) coupling simulation have significant advantages over traditional methods. In the present paper, the hydrodynamic and structural response characteristics of a large multi-body floating offshore structure are studied using a CFD-FEA method, and the results are compared with those obtained by the potential-flow-based commercial code SESAM/WADAM, and a three-dimensional nonlinear hydroelastic analysis commercial code COMPASS-WALCS-NE. The comparison and the analysis of the results show that the CFD-FEA method presented in this study can well simulate the behavior of the hydroelastic responses of flexible floating structures and has the potential to capture complex nonlinear behaviors.