A mobile communication system and method for managing the base station identifiers is provided. The method includes transmitting macro base station information from a terminal to a first pico base station; transmitting a Neighbor Relation Table (NRT) including the macro base station information from the first pico base station to a Self Organizing Network (SON) server; determining, at the SON server, whether a second pico base station using same Physical Cell Identifier (PCI) as the first pico base station exists by comparing a previously stored NRT with the received NRT; and reallocating, at the SON server, upon determining that the second pico base station uses the same PCI as the first pico base station, new PCIs to the first and second pico base stations.