Shock wave induces boundary layer separation when back pressure is set at the nozzle outlet. However, the effects of the complex flow characteristics on energy conversion mechanisms and the non-equilibrium phase transitions are not fully understood. This study developed a physical model for the homogeneous condensation of water vapour. The accuracy of the model was verified through flow and condensation experiments. The findings indicate that vortex clusters enhance energy transfer near the shear layer when the boundary layer separates. The separation point represents the region with the highest entropy generation. The peak entropy value near the wall with an increase of 7.07% as back pressure decreases from 0.75 to 0.1 MPa. The significant discovery that shock wave has minimal influence on droplet evaporation when the back pressure is 0.15 MPa, and the liquefaction efficiency at the outlet peaks at 79.42%. Moreover, over-expansion of the gas mixture at the back pressure of 0.15 MPa can lower the total pressure loss from 72.89% to 62.96% compared with the back pressure of 0.25 MPa. These findings provide an effective theoretical basis for determining optimal back pressures to reduce total pressure loss and enhance the liquefaction efficiency of the nozzle.