A method of defining physical channel transmit/receiving timings and resource allocation is provided for use in a Time Division Duplex (TDD) communication system supporting carrier aggregation. A method for receiving, at a base station, a Hybrid Automatic Repeat Request (HARQ) acknowledgement from a terminal in a Time Division Duplex (TDD) system supporting carrier aggregation of a primary cell and at least one secondary cell includes transmitting a downlink physical channel through one of the primary and secondary cells, receiving the HARQ acknowledgement corresponding to the downlink physical channel of the primary cell at a first timing predetermined for the primary cell, and receiving the HARQ acknowledgement corresponding to the downlink physical channel of the secondary cell at second timing, wherein the second timing is determined according to the first timing.