The prime objective of this investigation is to ascertain the stress analysis of dissimilar pistons with different compression ratios. The diverse piston geometries of Deep Cylindrical Piston (DCP), Shallow Re-Entrant Piston (SRP) which was exclusively designed by the base line of Hemispherical Existing Piston (HEP) at different compression ratios of 15:1, 17:1 and 16:1 respectively. The combustion characteristics of cylinder pressures were established for various piston geometries using different biodiesel blends of soya bean, rice bran and pongamia. The engine operating characteristics and load capacity in terms of the pressure with respect to crank angle rotation, air and fuel mixing rate and turning moments were attained from the experimental investigation. Analysis of piston geometry was done with boundary conditions of the maximum value of the cylinder pressure for pongamia biodiesel blends with diesel. The structural analysis of equivalent stress and total deformation values were plotted against the cylinder pressure values. This analysis predicts the portion of the piston structure that might be damaged on top or bottom skirt. Finally, mechanical thermal stresses developed in the piston was optimized with lesser deformation by Finite Element Analysis (FEM). © 2019 Elsevier Ltd.