Day to day rise in fuel price, stringent emission norms and power requirements makes the researchers for alternative fuel. The biodiesel performance in variable compression ratio (VCR) engine provides the equivalent performance in fuel requirements. Nanoparticles plays major role in combustion characteristics of engine analysis. Different nanoparticles with 75ppm under varying compression ratio from 16:1 to 19:1 for combination of loads. Waste cooking oil methyl ester (WCOME) attracts a wide attention in towards its availability in India and its inherent properties comprehend with diesel. The nanoparticles are prepared and blended using ultrasonication process. Then, the Experiment is designed using Taguchi design and the results will be compared with predicted results. The results show significant reduction in carbon monoxide (CO), hydrocarbon (HC and smoke are recorded with slight increase in Nitrogen oxides (NOx) emission. The error obtained is less than 5% for all predicted responses. The robust design will be useful for predicting the engine performance with minimum cost. The experiment is first designed using design of experiments (DOE) using Minitab17 version. The variables are used as Compression ratio, load and different nano-particles under three level and three factor designs. The expected responses are brake thermal efficiency, fuel consumption, exergy efficiency, entropy generation and CO, HC, NOx and smoke emissions.