The partially hydrogenated soybean methyl ester (PHSME) is produced from soybean methyl ester (SME) via catalytic transfer hydrogenation. It is revealed that after the catalytic transfer hydrogenation of SME, the high unsaturated components are selectively converted to low unsaturated or saturated components by Gas Chromatography-Mass Spectrometer (GC-MS) analysis. Although the kinematic viscosity of PHSME is increased slightly, its oxidation stability is improved significantly, and the cetane number of PHSME rises to a desirable level as well. Based on the analysis of thermogravimetry-differential scanning calorimeter (TG-DSC), it is found that PHSME has a greater average oxidation rate. In summary, the hydrogenated biodiesel has excellent ignition characteristic.