The fuel crisis throughout the world made many countries to be aware of their vulnerability to oil shortages. So many researches are still in progress and focus on the growth of bio fuel usage. In this regard, alternative fuels and the drivetrain play a major rule in critical emission issues. However, at the same time, enormous and vast number of vehicles have started to claim and place their heavy demand for alternative sources of fuel. Of course, gasoline and diesel, the conventional fuels will become scarce and much costlier. With a present known reserves and steep rise of demand and rate of consumption, hope of crude oil import is not going to last long. The CFD investigation is to find the combustion characteristics of the BioFuel with the various compositions of mixing with diesel, the Kirloskar IC Engine is taken for this research and the results of pressure, velocity, turbulence kinetic energy, temperature gradients, fuel combustions, oxidizers volume fractions also obtained from the CFD analysis results. CFD Analysis of Biodiesel combustion done in ANSYS Fluent. Software modeling of IC Engine done in CATIA V5 Software. Jatropha Methyl Ester (JME) and Mahua Methyl Ester (MME) are used for this research. Combustion characteristics in addition to emission parameters are assessed then a conclusion can be drawn.