A method of handling a communication operation of a mobile device in a wireless communication system, applicable to the mobile device which is configured with a plurality of serving cells comprising a first serving cell and a second serving cell by a network of the wireless communication system, the method comprising: receiving a first transmission in a first subframe via the first serving cell, wherein more than one serving cells are aggregated to achieve a wider band transmission in the wireless communication system and decoding the first transmission; generating a decoding result in response to decoding the first transmission; storing at least one soft channel bit of the first transmission in at least one partition of a soft buffer if the first transmission is not successfully decoded, wherein the soft buffer is divided into the plurality of partitions according to at least N soft, N DL licensed cells, M DL_HARQ, and M limit, wherein N soft is a size of the soft buffer, N DL licensed cells is a number of licensed serving cells configured to the mobile device, M DL_HARQ is a maximum number of DL HARQ processes and M limit is a constant or a configurable parameter, wherein M limit is determined according to at least one of the following: whether one of the licensed serving cells assists one of unlicensed serving cells; a number of unlicensed serving cells configured to the mobile device; a traffic load category of the one of the unlicensed serving cells; a congestion rate of the one of the unlicensed serving cells; and a permutation of the traffic load category and the number of the unlicensed serving cells; transmitting an acknowledgement,ACK, or negative-acknowledgement,NACK, in a second subframe, wherein the ACK or NACK corresponds to the decoding result; and receiving a second transmission in a third subframe via the second serving cell, wherein the second transmission is a retransmission of the first transmission. receiving a first transmission in a first subframe via the first serving cell, wherein more than one serving cells are aggregated to achieve a wider band transmission in the wireless communication system and decoding the first transmission; generating a decoding result in response to decoding the first transmission; storing at least one soft channel bit of the first transmission in at least one partition of a soft buffer if the first transmission is not successfully decoded, wherein the soft buffer is divided into the plurality of partitions according to at least N soft, N DL licensed cells, M DL_HARQ, and M limit, wherein N soft is a size of the soft buffer, N DL licensed cells is a number of licensed serving cells configured to the mobile device, M DL_HARQ is a maximum number of DL HARQ processes and M limit is a constant or a configurable parameter, wherein M limit is determined according to at least one of the following: whether one of the licensed serving cells assists one of unlicensed serving cells; a number of unlicensed serving cells configured to the mobile device; a traffic load category of the one of the unlicensed serving cells; a congestion rate of the one of the unlicensed serving cells; and a permutation of the traffic load category and the number of the unlicensed serving cells; whether one of the licensed serving cells assists one of unlicensed serving cells; a number of unlicensed serving cells configured to the mobile device; a traffic load category of the one of the unlicensed serving cells; a congestion rate of the one of the unlicensed serving cells; and a permutation of the traffic load category and the number of the unlicensed serving cells; transmitting an acknowledgement,ACK, or negative-acknowledgement,NACK, in a second subframe, wherein the ACK or NACK corresponds to the decoding result; and receiving a second transmission in a third subframe via the second serving cell, wherein the second transmission is a retransmission of the first transmission.