The effects of an electric supercharger (eS) and a dual-loop exhaust gas recirculation (EGR) system on a passenger car’s diesel engine’s emissions and fuel efficiency under various worldwide harmonized light-duty vehicles test procedure (WLTP) reference operation points were investigated using a one-dimensional engine cycle simulation, called GT-Power. After heavy EGR application, the in-cylinder pressure and temperature declined due to a dilution effect. As eS power and rpm increased, the brake-specific fuel consumption (BSFC) decreased because the effects of the air flow rate increased. However, it was unavoidable that nitrogen oxide (NOx) emissions also increased due to the higher in-cylinder pressure and temperature. To induce more EGR to the intake system, a dual-loop EGR system was applied with eS at different low-pressure EGR (LP-EGR) fractions (0, 0.25, 0.5, 0.75, and 1.0). Under these conditions, a design of experiment (DoE) procedure was carried out and response surface plots of the BSFC and brake-specific NOx (BSNOx) were prepared. A multi-objective Pareto optimization method was used to improve the trade-off in results between the BSFC and BSNOx. Through optimization, optimal Pareto fronts were obtained, which suggested design parameters for eS power and rpm to control the engine under various LP fraction conditions.