In this study, a 3D numerical model was used to predict nonlinear wave forces on a cylindrical pile installed in a shallow water region. The model was based on solving the viscous and incompressible Navier-Stokes equations for a two-phase flow (water and air) model and the volume of fluid method for treating the free surface of water. A new application was developed based on the cut-cell method to allow easy installation of complicated obstacles (e.g., bottom geometry and cylindrical pile) in a computational domain. Free-surface elevation, water particle velocities, and inline wave forces were calculated, and the results show good agreement with experimental data obtained by the Danish Hydraulic Institute. The simulation results revealed that the proposed model can, without the use of empirical formulas (i.e., Morison equation) and additional wave analysis models, reliably predict non-linear wave forces on an offshore wind turbine foundation installed in a shallow water region.