Thermodynamic simulation programs are widely used for designing complex thermal Systems, but most of them do not incorporate second law optimization techniques. In this study, an efficient optimization strategy is presented, which integrates three optimization techniques with a professional power plant and a cogeneration simulator so as to perform exergoeconomic optimization of complex thermal systems and generate combined pinch and exergy representations. This paper deals with the application of an evolutionary algorithm based on NSGA-II to multi-objective thermoeconomic optimization of coupling desalination plant with pressurized water reactor (PWR). In addition, one-objective thermoeconomic optimization through genetic algorithm and mixed integer non-linear mathematical programming methods has been applied for evaluation of multi-objective optimization. The thermodynamic simulation of this plant has been performed in the THERMOFLEX simulator. An Excel Add-in called THERMOFLEX link has been developed to Calculate the exergy of each stream from THERMOFLEX Simulation results. In addition, a computer code has been developed for thermoeconomic and improved combined pinch-exergy analysis in the MATLAB environment. Also, multi-objective and one-objective evolutionary algorithm optimization has been performed in MATLAB and one-objective mathematical programming has been performed in LINGO software. Both the design configuration and the process variables are optimized Simultaneously. The optimization algorithm can choose among several design options included in a Superstructure of the feed water heaters and multistage flash desalination in a dual-purpose plant. For the assumptions and simplifications made in this study, a 3000 MWh PWR power plant similar to Bushehr power plant has been considered. Copyright (C) 2008 John Wiley & Sons, Ltd.