Abstract: The relation between molybdenum and boron and nitrogen metabolism of three soybean varieties in each growth stage with five levels of molybdenum and boron was studied. The results showed that root activities, biomass of nodule, nitrate reductase activity and contents of total N in leaves were increased and contents of NO3-N in leaves were reduced with molybdenum or boron application. Furthermore, effect of molybdenum on nitrogen metabolism of soybean was higher than that of boron and the relation between molybdenum and boron on nitrogen metabolism of soybean was positive correlation. The results also indicated that three soybean varieties had some genetic variation of molybdenum and boron on nitrogen metabolism of soybean.