In this paper, a thermoeconomic model of a dual loop organic Rankine cycle (ORC) system has been developed to analyze both the thermodynamic and economic performance of several working fluid groups for the purpose of compressed natural gas (CNG) engine waste heat recovery. The effects of six key parameters on the thermoeconomic indicators of the dual loop ORC system are investigated. Furthermore, a multi-objective genetic algorithm (GA) is employed to solve the Pareto optimal solutions from the viewpoints of maximizing net power output and minimizing total investment post over the whole operating range of the CNG engine. The most suitable working fluid group is screened out, then the optimal parameter regions are determined. The results show that a higher evaporation pressure and a lower condensation temperature exhibit a positive effect on the thermoeconomic performances of the dual loop ORC system while the effects of variation in superheat degree and exhaust outlet temperature on the thermoeconomic performances are not obvious. The optimal evaporation pressure of the high temperature loop ORC (HT cycle) is always above 2.5 MPa. The optimal condensation temperature of the HT cycle, optimal evaporation temperature and condensation temperature of the low temperature loop ORC (LT cycle) are all kept almost constants. In addition, the optimal exhaust outlet temperature is mainly influenced by the engine speed. At the rated condition, the dual loop ORC system has the maximum net power output of 23.62 kW and the minimum electricity production cost (EPC) of 0.41 $/kW h. The thermal efficiency of the dual loop ORC system is in the range of 8.97-10.19% over the whole operating range.