There are provided a method for managing neighbor Base Station (BS) information in a mobile communication system, and a system thereof. A femto Access Service Network-Gateway (ASN-GW) controls at least one femto BS, manages scan information that an MS served by a macro BS requires in measuring at least one signal strength by scanning the at least one femto BS, creates the scan information in a format of Downlink Channel Descriptor (DCD) and Uplink Channel Descriptor (UCD) information, and transmits the scan information to the macro BS. The macro BS periodically broadcasts neighbor BS information of the femto BS, which includes the scan information, to MSs in its coverage using a Neighbor Advertisement (NBR-ADV) message.