The objective of this research work is to improve the in-cylinder air flow for facilitate better mixing and ultimately achieve complete combustion. From the literature it is revealed that the bowl shape of the piston has influence on creating effective swirl, tumble, and cross tumble motions during intake and initial stages of compression stroke. Different types of combustion chambers have been designed by keeping the same bowl volume to maintain the constant compression ratio and to ensure that the improvement is only due to geometric parameters such as bulge diameter, lip distance, and bowl to bore diameter ratio. Simulation work is carried out using ANSYS Fluent 14.5 computational fluid dynamics tool. The influence of these parameters on in-cylinder flow was also studied in this paper. The values of swirl, tumble, and cross tumble were calculated. Further to ensure the results of theoretical simulation a modified re-entrant combustion chamber was fabricated and the experimental work has been carried out in Kirloskar TAF 1 single cylinder, 4-stroke, compression ignition engine for diesel and jatropha methyl ester blend 20%. The experimental results were compared with the conventional chamber. It is found that the modified re-entrant chamber improves the brake thermal efficiency and reduced HC, CO, and smoke emissions of diesel and jatropha methyl ester blend 20% for all the tested conditions when compared to the conventional chamber.