A method and apparatus for transmitting reception acknowledgment for hybrid automatic repeat request (HARQ) in a wireless communication system are provided. A user equipment receives a plurality of downlink resource allocations on a plurality of downlink control channels by using a plurality of downlink carriers, and receives a plurality of downlink transfer blocks on a plurality of downlink shared channels indicated by the plurality of downlink resource allocations. The user equipment determines a plurality of acknowledgment (ACK)/negative acknowledgment (NACK) resource indices based on a plurality of resource indices obtained from downlink resources which use the plurality of downlink control channels. The user equipment transmits ACK/NACK for the plurality of downlink transfer blocks by using ACK/NACK resources indicated by the plurality of ACK/NACK resource indices.