An apparatus and method for supporting cells with different characteristics in a wireless communication system are provided. To operate for communications in a frame divided into a first part of a system common signal structure and a second part of a communication environment-dependent signal structure in a wireless communication system in which cells co-exist under different communication environments, a BS generates physical configuration information about a signal of the second part, transmits the physical configuration information about the signal of the second part in the first part, and conducts communications by processing signals transmitted and received in the second part according to the physical configuration information.