The sources of fossil fuels are depleting, their prices are increasing also harmful emissions are disturbing nature cycle, so necessity of using alternative fuels is increasing. Biodiesel stands as significant alternative fuel to diesel as thermophysical properties of biodiesel are nearer to diesel and it can be used in VCR diesel engines efficiently with proper selection of engine variables. The purpose of experimentation is to study the effect on thermal performance and emissions of Karanja oil biodiesel due to addition of Cocklebur biodiesel. In the present research work experimentation is conducted by blending Cocklebur seed oil biodiesel (20%) with Karanja oil biodiesel (80%) in VCR diesel engine altering engine variables CR, IP, IT and EGR for determining optimum conditions with best thermal performance, least emissions and compare with Karanja oil biodiesel. Taguchi Design L9 (34) Orthogonal array is applied for maximum BTE, minimum BSEC along with minimum pollutants like CO, HC, smoke and NOx. It is found that Engine operating variables are same for both the fuels except IP. It is concluded that BTE increases by 0.98% when 20% Cocklebur biodiesel is blended with Karanja biodiesel.