The invention discloses a data protection system and method for an iBeacon base station. The system comprises a server and at least one iBeacon base station, wherein the iBeacon base station comprises a wireless communication module and a control module, and the wireless communication module is configured to be in communication with the server and electrically connected with the control module so as to achieve data exchange between the server and the control module; the control module is configured to change identification information of the iBeacon base station and upload change information including the changed identification information to the server. A mapping table of the corresponding relation between the position information and the identification information of the iBeacon base station is updated and stored by the server according to the change information. Because the corresponding relation between the position information and the identification information of the iBeacon base station changes frequently, the risk that data of the iBeacon base station are illegally used can be reduced, human intervention is reduced, operation is simplified and efficiency is improved.