A method of controlling an operation of a small Base Station (BS) and the small BS in a communication system are provided. The method includes measuring the strengths of signals received from adjacent macro BSs, transmitting a reference signal corresponding to an Identifier (ID) of the small BS at a predetermined time, if a highest of the measured signal strengths received from the adjacent macro BSs is less than a threshold, and operating the small BS in an active mode, upon receipt of an activation signal from at least one Mobile Station (MS). The active mode is a state in which the small BS communicates with an MS within a service area of the small BS.