An interference management method for a wireless communication system, an anchor apparatus, a base station and a wireless communication system thereof are provided. The method includes the following steps. Receiving at least one base station information from the plurality of base stations. Finding at least one interference relationship of the base stations according to the base station information, and grouping the base stations into the at least one cluster according to the interference relationship. Each of the at least one cluster includes at least one base station. Deciding a selected group of uplink-downlink (UL-DL) configurations related to one or more clusters of the at least one cluster, wherein the selected group includes at least one of the UL-DL configurations. And, informing the base stations in at least one cluster to adjust the UL-DL configurations of the base stations according to the selected group of UL-DL configurations.