In Direct Injection (DI) diesel engines, combustion gets affected by change in in-cylinder air motion and Fuel injection system characteristics. Computational Fluid Dynamics (CFD) based models give detailed insight into the combustion phenomena. The present work investigates the effect of different combustion chamber geometries and fuel injection system parameters on engine emissions and performance aiming to improve trade-off between NOx and smoke. AVL FIRE CFD software is used in this work. Research engine having 9 liter capacity of heavy duty application has been selected for the study. Seven hole injector is used with mechanical fuel injection system having 1000 bar maximum pressure capability. Inputs required to model complex combustion process in the AVL FIRE are derived from one dimensional engine simulation software AVL BOOST. Experimental data required for making simulation models has been collected using experimental set up compliant to standards ISO 8178 which has been designed for off-road application. A basic reentrant bowl modeled and meshed in the software. After matching the simulation and experimental results of base cavity; flow and local emission generation phenomena have been studied. Various cavity shapes have been designed by maintaining the same cavity volume. Designed cavities simulated in the AVL FIRE. Combustion chamber giving the best results used further to study the effect of fuel injection system parameters. Best results obtained from combustion chamber shape and fuel injection system combination verified experimentally. This study reveals approach of using engine simulation tools in improving fuel economy and engine out emissions.