Based on the Navier-Stokes (RANS) equations, a three-dimensional (3-D) mathematical model for the hydrodynamics and structural dynamics of a floating point-absorbing wave energy converter (WEC) with a stroke control system in irregular and extreme waves is presented. The model is validated by a comparison of the numerical results with the wave tank experiment results of other researchers. The validated model is then utilized to examine the effect of wave height on structure displacements and connection rope tension. In the examined cases, the differences in WEC’s performance exhibited by an inviscid fluid and a viscous fluid can be neglected. Our results also reveal that the differences in behavior predicted by boundary element method (BEM) and the RANS-based method can be significant and vary considerably, depending on wave height.