A method of handling multi-access (MA) Protocol data unit (PDU) session under inter-system change is proposed. An MA PDU session uses one 3GPP access network or one non-3GPP access network at a time, or simultaneously one 3GPP access network and one non-3GPP access network. The UE and network can support Access Traffic Steering Switching and Splitting (ATSSS) functionalities to distribute traffic over 3GPP access and non-3GPP access for the established MA PDU session. Upon intersystem change from 5GS to EPS over the 3GPP access, the 3GPP part of an MA PDU session is transferred to a PDN connection, and the non-3GPP part of the MA PDU session is released. The QoS flows of the MA PDU session over both 3GPP access type and non-3GPP access type are transferred to the EPS bearer contexts of the corresponding PDN connection.