An apparatus and method of providing relay service in a broadband wireless access (BWA) communication are provided. The communication method includes dividing an entire frequency band into a plurality of bands to support a plurality of links; determining subcarrier allocation schemes for the divided bands independently from one another; and communicating using the determined subcarrier allocation schemes by the plurality of the links.When the direct link and the relay link are distinguished through the frequency multiplexing in the multihop relay BWA communication system, the present invention enables the independent channel estimation from the relay link by adopting the dedicated pilot based permutation scheme for the relay link.