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The energy crisis combined with increasingly severe environment pollution have highlighted the significance of the energy conservation and emission reduction in shipping industry. To improve the energy utilization rate and reduce pollution, a dual-pressure organic Rankine cycle system is proposed to reuse the heat of exhaust gas in marine engines. Many researches focused on the thermodynamics and thermos-economics of the waste heat recovery system, and optimized it from these two goals to recover more energy and decrease cost. However, the impact of the system itself on the environment, which was significant to assess the greenness, was often neglected in these studies. The system with high energy recovery rate may also cause serious environment pollution in the manufacturing or operation process, hence the environmental factor should be taken into account in the optimization. To solve the problems, an evaluation method combined thermodynamics, economics and environment is proposed. The parametric study of the dual-pressure organic Rankine cycle system with six common used working fluids is assessed by this method. Finally, taking the indicators of evaluation method as objective function, the multi-objective optimization method is conducted to figure out the optimum operation conditions for the system. Results show cyclopentane is the optimal working fluid considering thermodynamic, economic and environmental properties. Under the conditions of the evaporation pressure in high-pressure circuit 2.79 MPa, the evaporation pressure in low-pressure circuit 1.97 MPa, the condensation temperature 35 °C, the superheating temperature 1.2 °C, the system obtains a good performance with exergy efficiency 60.24%, electricity production cost 0.167 $/kWh and the environmental impact of net power output 11831.9 mPts/GJ.