A system and method for transmitting multi-carriers in a wireless communication system with a relay are provided. The method includes configuring each of downlink carriers that form the multi-carriers as at least one normal sub-frame and at least one backhaul sub-frame; determining one of the downlink carriers that has a maximum number of backhaul sub-frames, as a primary carrier, and other downlink carriers as sub-carriers; and altering a backhaul sub-frame into a normal sub-carrier in the sub-carrier, in response to a normal sub-frame of the primary carrier.