The present invention relates to a method for allocating a frequency domain spread code in a base station of a multi-carrier code division multiple access (MC-CDMA) communication system. A code allocation priority is established based on interference between previously allocated spread codes and a newly allocated spread code so as to minimize the interference caused by channel fading or a synchronization error according to a transmitting or receiving timing offset when a scheduler of the base station in the MC-CDMA communication system allocates a subcarrier group to the plurality of user terminals or channels, and the spread code is allocated to the plurality of user terminals or channels according to the established priority, by the scheduler of the base station.