Disclosed are an apparatus and a method for generating a preamble sequence in an orthogonal frequency division multiplexing communication system including a reference base station and a plurality of non-reference base stations and employing m sub-carriers in a frequency domain. A reference preamble sequence having a length equal to n is generated and mapped on a one-to-one basis with n sub-carriers of the m sub-carriers. A final preamble sequence equivalent to the reference preamble sequence is generated when the base station is a reference base station, or a phase of the reference preamble sequence is shifted by a predetermined phase in order to generate a phase-shifted final preamble sequence when the base station is a non-reference base station, thereby minimizing interference between neighbor base stations.