A method for handling semi-persistent transmission resources in a network terminal of a wireless communication system is disclosed. The wireless communication system supports carrier aggregation and semi-persistent scheduling (SPS). Carrier aggregation enables a user equipment (UE) of the wireless communication system to perform transmission and/or reception using multiple carriers. The method includes steps of establishing an RRC connection via a cell containing an uplink carrier and a downlink carrier, configuring at least one downlink carrier to the UE via a first RRC message, and transmitting a physical downlink control channel (PDCCH) signaling addressed to an SPS cell radio network temporary identifier of the UE, to configure or reconfigure a semi-persistent transmission resource to the UE or to trigger an SPS retransmission.