This study investigated the interaction between containers under extreme hydrodynamic conditions modeled on tsunamis to assess whether the number and layout of containers affect their motion and to guide future studies on numerical simulations describing tsunami-debris motion. The three-dimensional Fluid–Structure–Sediment–Seabed Interaction Model (FS3M), which can compute tsunami–container interaction, was used as a numerical test model, and numerical results for the specific target of the simulation were compared with experimental data to check the validity and computational accuracy of the FS3M. The study showed that the number of rows (Nx), columns (Ny), and stacks (Nz) in the initial arrangement of containers constitute the main factor affecting the area where the containers spread and their drift motion velocity. An increase in Nx and Nz can effectively reduce the container drift velocity. Conversely, as Ny increases, the drift motion velocity of the center of gravity of the entire group increases. The results of this study can facilitate the development of more realistic building structure scenarios in future research that consider the proposed characteristic damage estimation and comprehensive assessment methods laid out herein.