A three-dimensional CIP (Constrained Interpolation Profile) method for highly nonlinear wave-body interaction problems is presented. In the current numerical model, the wave-body interaction problem is treated as a multiphase problem, which includes a liquid phase (water), a gas phase (air) and a solid phase (floating body). A CIP based finite difference calculations are carried out in a regular computation domain with a Cartesian grid system. The free surface is captured by CIP method with a sharpness enhancement technique. The solid body is represented by distribution of virtual particles on the surface. A couple of three-dimensional numerical simulations are carried out to validate the proposed 3-D numerical model.