© 2019 Institute of Marine Engineering, Science & Technology.Nowadays, shipping industry faces challenges of energy efficiency and reducing of fuel consumption. Moreover, Waste Heat Recovery Systems (WHRS) regarding energy efficiency have a larger focus to utilise the heat energy lost from all thermal processes from ship engines. WHRS is one of the best methods to reduce fuel consumption and implicitly emissions. Refrigeration system, which can be evaluated as one of these systems, has a high energy efficiency potential on ships. In this study, exergoeconomic and air emission analyses of a case study ship named M/V Ince Ilgaz have been performed by comparing Vapour Compression Refrigeration System (VCRS) and VCRS with WHRS on exergy destruction and Second Law Efficiency in case of variable sea water temperature with 15 different refrigerants. Furthermore, a novel proposed WHRS is used for preheating of an accommodation water which leads reducing of exergy destruction about 9.31–10.60% while using R134A refrigerant. The fuel consumption due to refrigerant compressor has a 36% increase with the 10°C increment of sea water temperature. The increase of CO2, SO2, NO x and Particular Matter (PM) emissions is found about 183.40, 3.10, 4.65 and 0.47 tonnes, by the increase of sea water temperature from 20°C to 30°C for the fleet of 15 ships, respectively. In conclusion, using waste heat recovery on refrigeration system could directly reduce fuel consumption and air emissions.