Provided are a method and apparatus for transmitting acknowledgement/not-acknowledgement (ACK/NACK) of a user equipment in a carrier aggregation system. The method includes: assigning first and second control regions as search spaces for a specific cell; detecting scheduling information with respect to the specific cell from the first control region and/or second control region; receiving a data channel from the specific cell on the basis of the scheduling information; and transmitting ACK/NACK indicating a reception acknowledgement for the data channel, wherein if the scheduling information is detected from the first control region, the ACK/NACK is transmitted using a radio resource linked to another radio resource used to receive the scheduling information, and wherein if the scheduling information is detected from the second control region, the ACK/NACK is transmitted using a pre-set radio resource through a higher layer signal.