Micro-cooling systems are compact refrigeration systems widely applicable in microchemical analysis, biomedicine, and microelectromechanical systems (MEMS). These systems rely on the use of micro-ejectors to achieve precise, fast, and reliable flow and temperature control. However, the efficiency of micro-cooling systems is hindered by spontaneous condensation occurring downstream of the nozzle throat and within the nozzle itself, impacting the performance of the micro-ejector. A micro-scale ejector mathematical model describing wet steam flow was simulated to investigate the steam condensation phenomenon and its influence on flow, incorporating equations for liquid phase mass fraction and droplet number density transfer. The simulation results of wet vapor flow and ideal gas flow were compared and analyzed. The findings revealed that the pressure at the micro-nozzle outlet exceeded predictions based on the ideal gas assumption, while the velocity fell below it. These discrepancies indicated that condensation of the working fluid reduces the pumping capacity and the efficiency of the micro-cooling system. Furthermore, simulations explored the impact of inlet pressure and temperature conditions on spontaneous condensation within the nozzle. The results demonstrated that the properties of the working fluid directly influence transonic flow condensation, underscoring the importance of selecting appropriate working fluid parameters for nozzle design to ensure nozzle stability and optimal micro-ejector operation.