A greenhouse sand culture experiment was conducted to study the effects of citric acid, oxalic acid, malic acid, and their mixture on the nitrogen accumulation, nodulation, and nitrogen fixation of soybean. After the application of test low molecular weight organic acids, the nitrogen accumulation in the aboveground part of soybean decreased by 17.6%-44.9% at seedling stage, 29.8%-88.4% at flowering stage, 9.18%-69.6% at podding stage, and 2.21%-41.7% at maturing stage). In the meanwhile, the nodule number, nitrogenase activity, and leghemoglobin content decreased by 11.4%-59.6%, 80.5%-91.7%, and 11.9%-59.9%, respectively, resulting in a significant decrease (9.71%-64.5%) of nitrogen fixation of soybean, compared with the control. The inhibitory effect of test low molecular weight organic acids increased with their increasing concentration. Oxalic acid had a higher inhibitory effect than citric acid and malic acid, and the mixture of the three organic acids had an enhanced inhibitory effect.