Soybean is grown around the world primarily as a protein source for human and livestock diet. The plant is also utilized as a nitrogen fertilizer substitute. Nitrogen availability is important in realizing the purposes. When inoculated with rhizobia, soybean plants can derive nitrogen from both minerals and biological nitrogen fixation (BNF). Studies have showed that high nitrogen fertilizers input will adversely affect plant growth and nodules’ ability to fix nitrogen gas. This inhibition may vary with different external nitrogen levels and inoculation with alternative rhizobium strains. Thus, it is necessary to find out an optimal level of inorganic nitrogen input and an efficient rhizobium strain. Our hydroponic experiment on soybean growth and BNF at five mineral nitrogen levels and with two rhizobium strains separately, confirmed that soybean growth is inhibited by extremely high or low external nitrogen levels, and BNF is similarly affected. It also concluded that the rhizobium strain of USDA110 is always more efficient than the strain of BXYD 3. High yield in soybean production or high value in green manure is a result of good efficiency of inorganic nitrogen utilization combining high benefit from BNF. Our results imply that excessive nitrogen fertilizer application should be prevented and inoculation with the rhizobium USDA110 should be adopted in order to achieve these goals.