In this study, an automated warehouse system with mixed loading is considered. The majority of previous studies considered assumptions that were similar to those for a single-shuttle system with single loading. Due to the increased number of items in recent years, storage assignment strategies with single loading are not feasible because of the shortage of storage racks. This study adopts a storage policy with mixed loading for an automated warehouse system, which enables the use of one warehouse. Additional movement and transshipment operations, which involve mixed loading, are considered in this paper.