A communication device for handling a Hybrid Automatic Repeat Request, HARQ, Round-trip Time, RTT, Timer for a narrow band internet of things, NB-IoT, system, comprising: a storage device, storing instructions of: receiving a first downlink, DL, control information, DCI, on a DL control channel transmitted by a base station, BS, or being configured with a configured DL assignment, wherein the first DCI or the configured DL assignment indicates a first DL transmission comprising at least one downlink transmission for a HARQ process of the communication device; and starting the HARQ RTT Timer for the HARQ process, wherein the HARQ RTT Timer counts a time duration from a (n+1)-th transmission time interval, TTI, to a (n+k+N+3+deltaPDCCH)-th TTI, wherein the n-th TTI comprises a last transmission of the HARQ process; and k is a first interval between the n-th TTI and a first start TTI of a HARQ feedback associated to the first DL transmission, and N is a transmission duration in a plurality of TTIs of the HARQ feedback, and the deltaPDCCH is a second interval from (a last TTI of the plurality of TTIs + 4 TTIs) to a second start TTI of a next Physical DL Control Channel, PDCCH, occasion or to a third start TTI of a next PDCCH candidate; and a processing circuit, coupled to the storage device, configured to execute the instructions stored in the storage device. a storage device, storing instructions of: receiving a first downlink, DL, control information, DCI, on a DL control channel transmitted by a base station, BS, or being configured with a configured DL assignment, wherein the first DCI or the configured DL assignment indicates a first DL transmission comprising at least one downlink transmission for a HARQ process of the communication device; and starting the HARQ RTT Timer for the HARQ process, wherein the HARQ RTT Timer counts a time duration from a (n+1)-th transmission time interval, TTI, to a (n+k+N+3+deltaPDCCH)-th TTI, wherein the n-th TTI comprises a last transmission of the HARQ process; and k is a first interval between the n-th TTI and a first start TTI of a HARQ feedback associated to the first DL transmission, and N is a transmission duration in a plurality of TTIs of the HARQ feedback, and the deltaPDCCH is a second interval from (a last TTI of the plurality of TTIs + 4 TTIs) to a second start TTI of a next Physical DL Control Channel, PDCCH, occasion or to a third start TTI of a next PDCCH candidate; and receiving a first downlink, DL, control information, DCI, on a DL control channel transmitted by a base station, BS, or being configured with a configured DL assignment, wherein the first DCI or the configured DL assignment indicates a first DL transmission comprising at least one downlink transmission for a HARQ process of the communication device; and starting the HARQ RTT Timer for the HARQ process, wherein the HARQ RTT Timer counts a time duration from a (n+1)-th transmission time interval, TTI, to a (n+k+N+3+deltaPDCCH)-th TTI, wherein the n-th TTI comprises a last transmission of the HARQ process; and k is a first interval between the n-th TTI and a first start TTI of a HARQ feedback associated to the first DL transmission, and N is a transmission duration in a plurality of TTIs of the HARQ feedback, and the deltaPDCCH is a second interval from (a last TTI of the plurality of TTIs + 4 TTIs) to a second start TTI of a next Physical DL Control Channel, PDCCH, occasion or to a third start TTI of a next PDCCH candidate; and a processing circuit, coupled to the storage device, configured to execute the instructions stored in the storage device.