An apparatus and a method of a macro terminal for controlling interference in a wireless communication system of a hierarchical cell structure are provided. The method includes setting measurement reporting configuration for a blanking trigger per measurement identifier allocated by a macro base station, measuring a receive signal strength of a neighbor base station, comparing the measured receive signal strength value with a reference receive signal strength value of the measurement reporting configuration for the blanking trigger, and according to a comparison result, transmitting to the macro base station, a measurement report message comprising a measurement identifier corresponding to the measurement reporting configuration for the blanking trigger of a pico base station.