The multi-effect distillation with thermal vapour compression (MED-TVC) desalination system is efficient to produce freshwater. The steam ejector performance is not fully understood as the phase transition has been ignored in many studies. The present work develops a two-phase condensing flow model to assess the steam ejector performance considering nonequilibrium condensation phenomena. The transition of the flow structure from an under-expanded flow to an over-expanded flow in the steam ejector is investigated in detail. We present that the maximum Mach number can reach 4.02 in the under-expanded flow, which is weakened to 2.88 in the over-expanded flow. The steam undergoes several expansion-compression processes in the steam ejector in the under-expanded flow, which induces the formation and evaporation of massive droplets. In the over-expanded flow, the steam is compressed and then expanded after leaving the primary nozzle and the condensation process is not observed in mixing and constant sections. The increasing suction chamber pressure significantly improves the entrainment ratio while leading to an increasing entropy loss coefficient. The entrainment ratio is improved from 0.25 for the under-expanded flow to 1.69 for the over-expanded flow, while the entropy loss increases from 0.081 for the under-expanded flow to 0.29 for the over-expanded flow. This indicates that the transition of the flow structure from an under-expanded flow to an over-expanded flow can entrain more steam from the last effect while causes more entropy losses in a steam ejector for the MED-TVC desalination system.