A method and system for operating cells in a network where macro cells and home cells coexist are provided. The method includes determining a first set of neighbor macro Base Stations (BSs) located within a predefined reference distance from a new macro BS to be newly installed, determining a second set of neighbor macro BSs having a cell region overlapping a region of a serving cell served by the new macro BS, detecting at least one sector including a contact with the cell region of the new macro BS within a cell region of each of the neighbor macro BSs in the second set, determining a neighbor cell set including the detected at least one sector, generating an initial Neighbor Relation Table (NRT) by mapping information about each of neighbor cells included in the neighbor cell set, IDentifiers (IDs) of neighbor macro BSs serving the neighbor cells, and a Physical Resource Cell IDentifier (PCID) allocated to each of the neighbor macro BSs, and providing the initial NRT to the new macro BS as neighbor BS information.