A wafer storage system includes a main rail, an overhead hoist transport (OHT) on the main rail, the OHT being configured to transfer at least one storage case with wafers, an interface port on at least one side of the main rail, an auxiliary rail on one side of the interface port, the auxiliary rail being parallel to the main rail, and the interface port being between the main rail and the auxiliary rail, an auxiliary transport on the auxiliary rail, the auxiliary transport being configured to move along the auxiliary rail and to move the at least one storage case, a storage shelf on at least one side of the auxiliary transport, the storage shelf being configured to store the at least one storage case, and a worktable on one side of the storage shelf, the storage shelf being between the worktable and the auxiliary transport.