An apparatus and method for supporting different frame structures in a broadband wireless communication system are provided. A communication method of a Base Station (BS) includes determining a frame structure to be provided. A MAP message including an indicator that indicates a new standard is generated, when the provided frame structure conforms to the new standard. The generated MAP message is transmitted by performing physical layer encoding thereon. Accordingly, signaling is defined to report a currently provided frame structure to an MS, and thus, a system can support different frame structures.