Numerous benchmark calculations have been performed on ship motions and loads in waves. However, there are usually significant differences between codes, even for programs based on the same theory, and it is often extremely difficult to identify the factors that cause such differences. In this paper, the authors present a formulation of the strip method and 3D method in such a way that the common parts between the two are emphasized, and then develop an integrated program that can handle the two methods (STFM and zero-speed Green's function method) based on this formulation. This approach enables the extraction of the differences in the ship response between the two methods caused by the pure difference in the hydrodynamic force of them, i.e., the 3D effect. A comparison using tank tests under a wide range of conditions is performed to clarify the estimation accuracy of the two methods and the tendency of the 3D effect for ship motion, hull-girder sectional force, and hydrodynamic pressure for a container ship and a VLCC.