Among different technologies in internal combustion engines, waste heat recovery from the lost energies has great potential to improve fuel economy and reduce CO2 emission. In the present work, to achieve the optimal design parameters for a waste heat recovery system of a gas engine, a multi-objective optimization evolutionary algorithm is employed. The system consists of different types and combinations of the Organic Rankine/Kalina cycle as the waste heat recovery system of gas engine exhaust gas and the waste heat of cooling water is recovered by the trilateral flash cycle. The objective functions are chosen to maximize exergy efficiency and minimize the specific investment cost of the system. Cyclohexane, Toluene, and Benzene have been investigated and compared to the organic Rankine cycle working fluid. To evaluate different cycle configurations and working fluids, the Pareto front solutions related to 18 studied cases are compared. Meanwhile, the “Linear Programming Technique for Multidimensional Analysis of Preference” decision-making approach has been used as an optimal point in all cases. This work is aimed to compare the optimal design operating conditions of the studied configurations to choose the best configuration for waste heat recovery from a gas engine. The results reveal that, among the decision parameters, the organic Rankine cycle turbine inlet temperature is the most important in terms of the specific investment cost of the system. Also, considering the exergy and energy efficiency of the system, organic Rankine cycle turbine inlet temperature as well as organic Rankine cycle and trilateral flash cycle turbine isentropic efficiencies are of great importance. The Pareto front comparison for each configuration indicates that toluene is the most suitable fluid for the organic Rankine cycle in all configurations. Comparing the selected optimal points in different combinations reveals that, the configuration of organic Rankine cycle with internal heat exchanger-trilateral flash cycle, due to its lower payback period and specific investment cost as well as the higher exergy efficiency and net power output in optimal point, is the prominent compared to the other combinations. Furthermore, the optimized configuration of the organic Rankine cycle with the internal heat exchanger-trilateral flash cycle shows a 14.31% increase in the exergy efficiency and an 8.2% decrease in the specific investment cost of the system compared to the base case. Employing the optimized configuration of the organic Rankine cycle with internal heat exchanger-trilateral flash cycle as waste heat recovery of the gas engine leads to a 7.8 kW increment of net power output, equivalent to an increase of 18.85% exergy efficiency of the whole system including engine and bottoming cycle. On the other hand, additional equipment to the engine, impose 3061$/kW specific investment cost which takes 2.2 years to be paid back.