Exhaust gas recirculation (EGR) has been an efficient emission treatment strategy employed in internal combustion engines (ICEs) to cope with NOx emission limits since the introduction of Euro 4 regulations for heavy-duty commercial vehicles. A portion of the exhaust gas is fed back into the intake port, replacing O2 in the fresh air with inert CO2 from the exhaust gas, resulting in a reduction in the combustion temperature and, hence, a reduction in NOx emissions. Considering the high exhaust temperature, this process increases the charge mixture temperature and degrades the volumetric efficiency of the engine. EGR coolers have been introduced as vital parts of EGR exhaust treatment systems with the aim of reducing the intake port temperature to increase volumetric efficiency and further reduce combustion temperatures. EGR coolers are heat exchangers (HXs) that generally employ engine coolant to reduce the EGR temperature with effectiveness values around 0.7~0.85 and downgrade with engine usage owing to soot deposition. Increasing the effectiveness of the EGR cooler has a positive effect on engine volumetric efficiency and reduces NOx, particulate matter (PM), and fuel consumption. The current study involved the design of a microchannel HX for a 500 PS heavy-duty Euro 6 diesel engine EGR cooler. The mechanical and thermal-hydraulic design calculations of the proposed HX were performed using Mathematica software. The optimum HX dimensions for the required boundary conditions were determined, and the performance of the EGR cooler was analyzed for the current and proposed options. Furthermore, Diesel-RK software was used to model the engine performance with NOx, PM, CO2 emissions, and fuel consumption predictions. The results show that the newly proposed microchannel HX design improves NOx, PM, and specific fuel consumption by 6.75%, 11.30%, and 0.65%, respectively.