A method of handling hybrid automatic repeat request, hereafter referred to as HARQ, acknowledgement responses in a network of a wireless communication system of a long-term evolution-advanced system, hereafter referred to as LTE-A, the method comprising assigning resources for a plurality of physical hybrid indicator channels, hereafter referred to as PHICHs, and a plurality of extended physical hybrid indicator channels, hereafter referred to as ePHICHs,; and transmitting a HARQ acknowledgement message to a communication device of the wireless communication system on a channel selected from the plurality of PHICHs and the plurality of ePHICHs, after receiving an uplink transmission from the communication device; wherein the network comprises a first component carrier and at least a second component carrier; wherein a configuration of the plurality of PHICHs and the plurality of ePHICHs is generated and sent to the communication device before transmitting the HARQ acknowledgement message to the communication device, such that the communication device is capable of receiving the HARQ acknowledgement message via the channel; wherein the network calculates a group index and a sequence index according to the following equations: n ̅ ePHICH group = I PRB RA lowest _ index + n DMRS mod N ePHICH group + I ePHICH N ePHICH group n ePHICH seq = ⌊ I PRB _ RA lowest _ index N ePHICH group ⌋ + n DMRS mod 2 N SF ePHICH I ePHICH = { 1, for TDD uplink / downlink configuration 0 with PUSCH transmission insubframe n = 4 or 9 0, otherwise N ePHICH group = N PHICH group n ePHICH group = f m = { n ̅ ePHICH group + ⌊ n ̅ ePHICH group N PHICH group ⌋ N PHICH group, m i = 2 & I ePHICH = 0 n ̅ ePHICH group − N ePHICH group − N PHICH group 1 − ⌊ n ̅ ePHICH group 2 N PHICH group ⌋, m i = 2 & I ePHICH = 1 n ̅ ePHICH group, otherwise wherein n ePHICH group denotes the group index, n ePHICH seq denotes the sequence index, N PHICH group denotes the total group number of the plurality of PHICHs, N ePHICH group denotes the total group number of the plurality of PHICHs and the plurality of ePHICHs, N SF PHICH denotes the spreading factor of the plurality of PHICHs, I PRB _ RA lowest _ index denotes the lowest uplink resource block index used for the corresponding uplink transmission, n DMRS denotes the parameter of demodulation reference signals which is configured for the uplink transmission, and m i denotes the factor of PHICH/ePHICH resource for a subframe i; wherein for a FDD system, m i = 1, and for a TDD system, m ¡ depends on the specified uplink-downlink configuration and the subframe i. assigning resources for a plurality of physical hybrid indicator channels, hereafter referred to as PHICHs, and a plurality of extended physical hybrid indicator channels, hereafter referred to as ePHICHs,; and transmitting a HARQ acknowledgement message to a communication device of the wireless communication system on a channel selected from the plurality of PHICHs and the plurality of ePHICHs, after receiving an uplink transmission from the communication device; wherein the network comprises a first component carrier and at least a second component carrier; wherein a configuration of the plurality of PHICHs and the plurality of ePHICHs is generated and sent to the communication device before transmitting the HARQ acknowledgement message to the communication device, such that the communication device is capable of receiving the HARQ acknowledgement message via the channel; wherein the network calculates a group index and a sequence index according to the following equations: n ̅ ePHICH group = I PRB RA lowest _ index + n DMRS mod N ePHICH group + I ePHICH N ePHICH group n ePHICH seq = ⌊ I PRB _ RA lowest _ index N ePHICH group ⌋ + n DMRS mod 2 N SF ePHICH I ePHICH = { 1, for TDD uplink / downlink configuration 0 with PUSCH transmission insubframe n = 4 or 9 0, otherwise N ePHICH group = N PHICH group n ePHICH group = f m = { n ̅ ePHICH group + ⌊ n ̅ ePHICH group N PHICH group ⌋ N PHICH group, m i = 2 & I ePHICH = 0 n ̅ ePHICH group − N ePHICH group − N PHICH group 1 − ⌊ n ̅ ePHICH group 2 N PHICH group ⌋, m i = 2 & I ePHICH = 1 n ̅ ePHICH group, otherwise wherein n ePHICH group denotes the group index, n ePHICH seq denotes the sequence index, N PHICH group denotes the total group number of the plurality of PHICHs, N ePHICH group denotes the total group number of the plurality of PHICHs and the plurality of ePHICHs, N SF PHICH denotes the spreading factor of the plurality of PHICHs, I PRB _ RA lowest _ index denotes the lowest uplink resource block index used for the corresponding uplink transmission, n DMRS denotes the parameter of demodulation reference signals which is configured for the uplink transmission, and m i denotes the factor of PHICH/ePHICH resource for a subframe i; wherein for a FDD system, m i = 1, and for a TDD system, m ¡ depends on the specified uplink-downlink configuration and the subframe i.