An apparatus and a method for selecting a candidate channel to change an operating channel so as to minimize effect of interference in a wireless communication system using a Cognitive Radio (CR) function are provided. The method includes confirming an operating channel of at least one neighbor cell and candidate channel set to a third group by the neighbor cell; setting a candidate channel used as the operating channel of the neighbor cell among at least one candidate channels changeable to the operating channel, to a third group of lowest priority; setting candidate channels set to the third group of the neighbor cell among candidate channels not set to the third group, to a second group; and setting candidate channels set to neither the second group nor the third group, to a first group of highest priority.