An apparatus and method for indicating a zone by a base station in a mobile communication system, in which a frame consists of an uplink sub-frame and a downlink sub-frame, and each of the uplink and downlink sub-frames includes a plurality of zones, are provided. The method includes identifying at least one of a channel condition of a mobile station, a condition on whether or not the mobile station supports inter-heterogeneous-network communication, a load condition of the base station, and a resource condition of a cell, determining if the mobile station can transmit/receive a signal through a number of zones that is less than the total number of zones based on the at least one identified condition and transmitting control information, which indicates a zone capable of being used for signal transmission/reception by the mobile station, to the mobile station, when the mobile station can transmit/receive the signal through the number of zones.