A method and apparatus for TDD inter-band carrier aggregation in a wireless communication system includes performing aggregating multiple cells with different TDD UL-DL configurations, transmitting a PUSCH transmission on a first cell, the subframe for HARQ feedback reception for the PUSCH in a first cell colliding with a UL subframe in a second cell, and performing one of setting the corresponding HARQ feedback to ACK, flushing the corresponding HARQ buffer, and changing the corresponding HARQ feedback subframe for the PUSCH to another subframe.