For the purpose of biofuel production for transportation from non-food biomass, production of high quality biodiesel fuel from Jatropha oil by the transesterification process and hydrocarbon fuel from Jatropha residue by the fast pyrolysis-upgrading process were developed. It was demonstrated that biodiesel fuel which was increased their oxidation stability and inhibited their cold flow properties by partial hydrogenation of polyunsaturated fatty acid methyl ester selective to monounsaturated compounds was provided in a pilot plant. On the other hand, hydrocarbon fuel was produced by the fast pyrolysis and bio-oil upgrading from Jatropha residues.