Exhaust gas recirculation (EGR) is an emission control technology allowing significant NOx emission reduction from light-and heavy duty diesel engines. The future EGR type, dual loop EGR, combining features of high pressure loop EGR and low pressure loop EGR, was developed and optimized by using a commercial engine simulation program, GT-POWER. Some variables were selected to control dual loop EGR system such as VGT (Variable Geometry Turbocharger)performance, especially turbo speed, flap valve opening diameter at the exhaust tail pipe, and EGR valve opening diameter. Applying the dual loop EGR system in the light-duty diesel engine might cause some problems, such as decrease of engine performance and increase of brake specific fuel consumption (BSFC). So proper EGR rate (or mass flow) control would be needed because there are trade-offs of two types of the EGR (HPL and LPL) features. In this study, a diesel engine under dual loop EGR system was optimized by using design of experiment (DoE). Some dominant variables were determined which had effects on torque, BSFC, NOx, and EGR rate. As a result, optimization was performed to compensate the torque and BSFC by controlling start of injection (SOI), injection mass and EGR valves, etc.