In this paper, three-dimensional free-surface flows are simulated by using two different numerical methods, the constrained interpolation profile (CIP)-based and finite volume (FV)-based methods. In the CIP-based method, the governing equations are solved on stationary staggered Cartesian grids by a finite difference method, and an immersed boundary technique is applied to deal with wave-body interactions. In the FV-based method, the governing equations are solved by applying collocated finite volume discretization, and body-fitted meshes are used. A free-surface boundary is considered as the interface of the multi-phase flow with air and water, and a volumeof-fluid (VOF) approach is applied to trace the free surface. Among many variations of the VOF-type method, the tangent of hyperbola for interface capturing (THINC) and the compressive interface capturing scheme for arbitrary meshes (CICSAM) techniques are used in the CIP-based method and FV-based method, respectively. Numerical simulations have been carried out for dam-breaking and wave-body interaction problems. The computational results of the two methods are compared with experimental data and their differences are observed.