A method and apparatus are disclosed from the perspective of a network node. In one embodiment, the method includes the network node transmitting a first message with a DRB (Data Radio Bearer) configuration to a UE (User Equipment) for establishing a default DRB for a PDU (Packet Data Unit) session, wherein the DRB configuration includes a QFI (QoS Flow Id) configuration used to indicate whether a QFI field is present or not in uplink for the default DRB and the QFI configuration is always set to a value indicating the QFI field is present in uplink for the default DRB. The method further includes the network node establishing the default DRB with a presence of the QFI field in uplink. The method also includes the network node receiving a SDAP (Service Data Adaptation Protocol) PDU with the QFI field via the default DRB from the UE.