In this work, using sodium borohydride as hydrogen donor instead of potentially dangerous hydrogen gas, and Ni-La-B as catalyst, a new method of partial hydrogenation of fatty acid methyl esters (FAMEs) was introduced as a mild process to gain the upgraded biodiesel. The effects of important operating parameters, including catalyst loading, reaction temperature, time, hydrogen donor amount and water quantity, have been investigated. Under the optimum conditions (catalyst loading 10 wt%, reaction time 150 min, reaction temperature 85 °C, sodium borohydride amount 1.14 g, and water quantity 100 g), the conversion ratio of methyl linoleate (C18:2) reached 95.4%, the iodine value of hydrogenated FAMEs decreased from 151.9 to 76.1, and good hydrogenation effect was achieved . Based on the results, the possible mechanisms were presented involved in the partial hydrogenation of FAMEs using sodium borohydride as hydrogen donor. Overall, a mild hydrogen way to upgrade the biodiesel and a systematic investigation to understand the hydrogenation reaction using sodium borohydride as hydrogen donor have been presented in the present work.