The present research develops a numerical fluid-structure interaction (FSI) code based on CFDShip-Iowa version 4, a general-purpose URANS/DES overset fluid solver. Linear and nonlinear FSI methods are developed to compute structural responses on surface ships or marine structures. The modal superposition transient analysis and the nonlinear FEM structure solver are used for small and large deformation FSI problems, respectively. The gluing method is applied to transfer the forces and displacements on non-matching grids for fluid and structure domains. The linear FEM solver is applied to deform the boundary layer grid with large deformation in the fluid domain, while the deformation is ignored in small deformation problems. Deformation of an interior point in the boundary layer grid is obtained using linear interpolation in both linear and nonlinear deformation problems. The S175 containership is studied in regular waves as an application example for the linear problem. Heave and pitch responses are compared with the experiments, showing good agreement. Time histories of vertical bending moment (VBM) are calculated using rigid model, one-way coupling, and two-way coupling approaches. The elastic models are able to capture the ringing of the VBM induced by slamming, while the rigid model shows a peak at the moment of slamming without further fluctuations. The two-way coupling method shows the effects of hull deformation on the amplitude and phase of VBM as well as the accelerations of heave and pitch. For the nonlinear deformation problem three sloshing tanks with an elastic bar clamped to its bottom or top are simulated and compared with the experiments and other numerical simulation results. The present simulation results show reasonable agreement with the experiments for bar deformation and free surface elevation. A secondary wave on the free surface is creadted by the vorticity generated from the free surface. The effect of the bar on the sloshing impact is studied comparing dynamic pressure acting on the tank wall without bar, with an elatic bar, and with a rigid bar.