The catalytic transfer hydrogenation (CTH) is a novel, alternative process for the selective hydrogenation, and the microwave is an effective heating method for organic reaction. In this study, CTH of Jatropha oil biodiesel was performed through the method of microwave heating using Raney-Ni as catalyst and water as solvent. The effect of operating parameters on the composition of upgraded biodiesel was analyzed in detail, and the optimum conditions for CTH of Jatropha oil biodiesel were obtained. Under the optimum conditions, the mass conversion ratio of methyl linoleate reached 91.98 wt% at reaction time of 50 min. For the upgraded biodiesel obtained at 50 min, the methyl linoleate content, the methyl oleate content, the methyl stearate content, and the iodine value were 2.45 wt%, 76.70 wt%, 8.45 wt%, and 70.21, respectively. The experimental data of CTH of Jatropha oil biodiesel under microwave heating were well described by pseudo-first order kinetic model, and the kinetic rate constants and the selectivity of CTH were gained. In view of high selectivity and high reaction rate, CTH using microwave energy as heating source, Raney-Ni as catalyst and water as solvent was found to be an effective approach for the catalytic upgrading of Jatropha oil biodiesel.