A base station, BS, for handling Physical Random Access Channel, PRACH, resources on a secondary cell, SCell, for a communication device in carrier aggregation, CA, comprising: at least one storage device; and at least one processing circuit, coupled to the at least one storage device, wherein the at least one storage device stores, and the at least one processing circuit is configured to execute, instructions of: transmitting a radio resource control, RRC, message configuring the SCell to the communication device, wherein the RRC message comprises a PRACH resources configuration for the SCell, a downlink, DL, beam management, BM, reference signal, RS, configuration for the SCell and an association between a plurality of PRACH resources and a plurality of DL transmission, Tx, beams; transmitting a plurality of DL BM RSs to the communication device by using the plurality of DL Tx beams on the SCell, respectively, according to the DL BM RS configuration; receiving a measurement report of the plurality of DL BM RSs from the communication device on a primary cell, PCell; determining a DL Tx beam of the plurality of DL Tx beams according to the measurement report; transmitting a Physical DL Control Channel, PDCCH, order to the communication device by using the DL Tx beam, wherein the PDCCH order comprises a PRACH mask index indicating at least one PRACH resource of the plurality of PRACH resources; and determining a PRACH resource indicated in the PDCCH order to the communication device according to the measurement report and the association. at least one storage device; and at least one processing circuit, coupled to the at least one storage device, wherein the at least one storage device stores, and the at least one processing circuit is configured to execute, instructions of: transmitting a radio resource control, RRC, message configuring the SCell to the communication device, wherein the RRC message comprises a PRACH resources configuration for the SCell, a downlink, DL, beam management, BM, reference signal, RS, configuration for the SCell and an association between a plurality of PRACH resources and a plurality of DL transmission, Tx, beams; transmitting a plurality of DL BM RSs to the communication device by using the plurality of DL Tx beams on the SCell, respectively, according to the DL BM RS configuration; receiving a measurement report of the plurality of DL BM RSs from the communication device on a primary cell, PCell; determining a DL Tx beam of the plurality of DL Tx beams according to the measurement report; transmitting a Physical DL Control Channel, PDCCH, order to the communication device by using the DL Tx beam, wherein the PDCCH order comprises a PRACH mask index indicating at least one PRACH resource of the plurality of PRACH resources; and determining a PRACH resource indicated in the PDCCH order to the communication device according to the measurement report and the association. transmitting a radio resource control, RRC, message configuring the SCell to the communication device, wherein the RRC message comprises a PRACH resources configuration for the SCell, a downlink, DL, beam management, BM, reference signal, RS, configuration for the SCell and an association between a plurality of PRACH resources and a plurality of DL transmission, Tx, beams; transmitting a plurality of DL BM RSs to the communication device by using the plurality of DL Tx beams on the SCell, respectively, according to the DL BM RS configuration; receiving a measurement report of the plurality of DL BM RSs from the communication device on a primary cell, PCell; determining a DL Tx beam of the plurality of DL Tx beams according to the measurement report; transmitting a Physical DL Control Channel, PDCCH, order to the communication device by using the DL Tx beam, wherein the PDCCH order comprises a PRACH mask index indicating at least one PRACH resource of the plurality of PRACH resources; and determining a PRACH resource indicated in the PDCCH order to the communication device according to the measurement report and the association.