A method of controlling a package storage system may include a storage unit that is loaded in a delivery vehicle and stores one or more packages. The method may include: receiving delivery information of the packages from a scanner; storing slot information of slots in which the packages are stored and the delivery information of the packages, in a matched manner; determining, on the basis of the delivery information and driving information of the delivery vehicle, the package to be withdrawn among the packages; and outputting, on the basis of the delivery information and the slot information, a notification command for providing a notification of the slot in which the package to be withdrawn is stored.