A resource allocation method and an apparatus for mitigating inter-cell interference in the heterogeneous cellular communication system are provided. The method for a first type base station to allocate resource in a wireless communication system including the first and second types base stations according to the present invention includes estimating an available Frequency Assignment (FA) not used by a neighbor second type terminal among FAs used by the first type base station, and allocating sub-channels associated with one of the available FAs not used by the neighbor second type terminal to a first type terminal, wherein the second type base station allocates the sub-channels for uplink and downlink transmissions of the second type terminal over a predetermined time period such that an FA in which sub-channels for the uplink transmissions are allocated and the FA in which sub-channels for the downlink transmissions are allocated are the same.