To study the response of two leguminous crops to nitrogen forms, the hydroponic culture experiments with the same strength of ammonium or nitrate as sole nitrogen nutrient were conducted, and the change of pH in solution was monitored in these seven days. Based on supplying ammonium alone, the response characteristics of ammonium of two legume crops under different pH (4.5 and 6.5) treatments have been studied. The expression of ammonium transporter (AMT) genes was analyzed by RT-PCR under different pH treatments. By constructing a phylogenetic tree, sequence alignment of key residues, the bioinformatics analysis of AMT proteins in different species was carried out. The results showed that, compared with nitrogen deficiency treatment, the biomass of soybean and common bean significantly increased under nitrate treatment, especially root biomass, but there was no significant change under ammonium treatment. However, the total nitrogen accumulation was similarly accumulated in plants under ammonium and nitrate treatment. The pH of the solution decreased significantly under ammonium treatment. By controlling the pH of the solution treated with ammonium, we found that the biomass of the two legumes was significantly reduced at pH 4.5 compared with that at pH 6.5. Results showed that the expression of most ammonium transporter genes was significantly reduced at pH 4.5 compared with pH 6.5. Bioinformatics analysis showed that the AMT of soybean and common bean was closer than that of rice. This study showed that the absorption of ammonium nitrogen by leguminous crops could lead to acidification of the rhizosphere environment and inhibit plant growth, which provided a perspective for improving nitrogen nutrition of leguminous crops in the field.