A complex Crank–Nicolson finite difference (CNFD) method is developed and is applied to solve numerical solution of three-dimensional potential flow equations. The CNFD method is applied to simulate evolution mechanism of 3D free surface wave. We develop a staggered mesh grid is arranged to locate the velocity field. 3D tank is mapped onto a cube with a σ transformation. The CNFD method is applied to discrete the system of potential flow formula and the iterative solutions are solved for potential flow formula, Poisson equation, and free surface kinematic equation. From the experimental results, the present result agrees with the previous publications. The evolution of complex waves is displayed with different time and wave length. The different wave elevation of free surface is displayed in detail in experimental process. The computation process requires a large amount of computational resources and time consuming.