Abstract: To calculate the forces acting on very large structures under the effects of waves, a three-dimensional numerical model based on the large eddy simulation (LES) method was developed, in which the σ-coordinate transformation was used to track time-dependent free surfaces and the immersed boundary method (IBM) was added to deal with irregular structure surfaces. To verify the accuracy of the numerical model, it was used to simulate regular wave diffraction around a large-diameter vertical circular cylinder. The numerical results for wave height around the cylinder agreed well with those from the analytical solution. Using the three-dimensional numerical model, wave interaction with a boxed steel cofferdam in South Pylon of the 3^rd Nanjing Changjiang River Bridge was simulated. The obtained wave forces agreed well with the experimental data, which means that the three-dimensional numerical model is capable of simulating the interaction between three-dimensional wave and very large structures in engineering.