The current work aims to analyse a two-stage vapour compression refrigeration (TSVCR) cycle for freeze desalination. In this system, a low-pressure reversible subsystem (LPS) performs simultaneous freezing-thawing. The high-pressure subsystem (HPS) ensures cycle thermal stability. A mathematical model is developed to evaluate energy and exergy performance. Three eco-friendly refrigerants [R1234ze(E), R1234yf and R1243zf] are considered and compared with R22. The results show COP ranging from 6.5 to 12.7, with a specific energy consumption of 8.2 to 14.8 kWh/m3 of freshwater. The highest exergy efficiency of 38.4% is reported for R1243zf, which is higher by 1-3%, compared to R22 and R1234ze(E). However, R1234yf exhibits 11.14% and 7.8% lower energy and exergy performance. The maximum exergy destruction arises from the low pressure compressor (29%) followed by the latent heat condenser (23%). The uncondensed refrigerant significantly affects the performance and thermal stability. The study shows R1243zf and R1234ze are good alternatives to R22 due to their better energy and exergy performance.