Organic Rankine Cycle waste heat recovery has recently been one of the most promising technologies for enhancing ship energy efficiency. This study investigates the thermodynamic and environmental performance of an ORC-based exhaust gas waste heat recovery system integrated with a methanol-fueled marine engine. Hydrocarbons of pentane and cyclopentane are mixed with R1336mzz(Z), a flame-retardant working fluid, improving safety and operational stability. The effects of temperature glide, mass fraction and evaporation pressure of zeotropic working fluids on the thermodynamic performance are analysed. This study aims to evaluate the energy efficiency, exergy performance, and environmental impact of hydrocarbon mixtures with R1336mzz(Z), and show the feasibility and potential of zeotropic mixtures for sustainable shipboard applications. Unlike most research in this field, an energy-efficient, non-flammable, very low GWP (<5) and zero ODP hydrofluoroolefin is used to mix with hydrocarbons. According to the results, zeotropic mixtures have higher thermal and exergy efficiency than pure R1336mzz(Z). Using R1336mzz(Z)/cyclopentane (0.3/0.7) as the working fluid, thermal and exergy efficiencies can be increased by more than 6%, preventing approximately 750 tons of CO2 per year.