An apparatus and a method for transmitting ACKnowledge (ACK) channels by a Relay Station (RS) in a wireless communication system are provided. The method includes, when receiving one or more ACK information from one or more lower nodes, checking ACK channel constitution information provided from an upper node, arranging one or more ACK channels to transmit corresponding ACK information according to the ACK channel constitution information by distinguishing ACK information of one or more data scheduled by the upper node and ACK information of one or more retransmission data not scheduled by the upper node, and transmitting the one or more ACK information to the upper node in the arranged ACK channels.