A numerical study of NOx reduction for a Direct Injection (DI) Diesel engine with complex geometry, which includes intake/exhaust ports and moving valves, was carried out using the commercial computational fluid dynamics software KIVA-3v. The numerical simulations were conducted to investigate the effects of engine operating and geometrical parameters, including fuel injection timing, fuel injection duration, and piston bowl depth, on the NOx formation and the thermal efficiency of the DI Diesel engine. The tradeoff relationships between the reduction in NOx and the decrease in thermal efficiency were established.