From International Energy Statistics (IES) survey, China, US and India are top three countries in emitting CO2 emissions. Further, worldwide national governments are focused to control CO2 emissions at source by stringent regulatory limits. OEMs and Research laboratories are working on several technology options such as advanced fuel injection system, optimizing in cylinder combustion system, thermal management and reduced engine friction to meet this legal requirements.In this paper, research work focused on improving combustion system through selection optimum bowl geometry and increasing volumetric efficiency through valve timings, profile and intake system using both 1D and 3D-CFD numerical approach. The main objective of this approach to utilize fossil fuel to its maximum potential in a single cylinder Naturally Aspirated (NA) water cooled engine with CRDI. In first step, The optimum combustion bowl parameters like Bowl diameter / Bore ratio, Bowl Depth / Bore ratio, Pip height and Re-entrance ratio were optimized and 4% improvement in BSFC was observed. In 2nd step, optimum valve timings, profile and intake system tuning, the volumetric efficiency of base engine increased by 5% at higher speed zone and not significant improvement was observed at low speed zone. The single cylinder engine by optimizing the valve timing. The combined combustion bowl and valve timings changes have shown significant reduction in smoke and BSFC over entire engine operating zone. Combined use of 1D and 3D-CFD tools supported in selection of optimum system to reduce fuel consumption and lower emissions through combustion system development.