Methods and systems for a MTRS with an ejector system are provided. The system can include a refrigeration circuit that has a compressor, a first heat exchanger downstream of the compressor, first and second heat exchange units downstream of the first heat exchanger, and an ejector system downstream of the first and second heat exchange units and upstream of the compressor. The first heat exchange unit provides independent climate control to a first zone of the transport unit. The second heat exchange unit provides independent climate control to a second zone of the transport unit. The ejector system mixes refrigerant exiting the first heat exchange unit with refrigerant exiting the second heat exchange unit, increases the pressure of the mixed refrigerant, and directs the mixed refrigerant to the compressor.