This study aims to determine variability among soybean (Glycine max (L.) Merr.) cultivars under drought conditions and how nitrogen metabolites, metabolism-related enzymes, and gene expression vary during soybean growth. Three soybean cultivars, Shennong17 (CV.SN17), Shennong8 (CV.SN8), and Shennong12 (CV.SN12), were grown in pot culture and subjected to drought stress at reproductive stages for 45 days. The results showed that long-term drought stress decreased biomass allocation to reproductive organs, weakened antioxidant capacity, and reduced seed weight, effects that were less pronounced in CV.SN12 compared with those in CV.SN8 and CV.SN17. Drought stress decreased the concentrations of nitrogen and soluble protein but increased nitrate concentration in leaves. This was related to the significantly reduction of nitrogen metabolism efficiency, including decreased activities of nitrogen metabolism enzymes, and downregulated expression of GmNR, GmNiR, GmGS, and GmGOGAT. Drought stress increased the concentrations of free amino acid, proline, and soluble sugar in leaves to enhance the osmotic adjustment ability. Furthermore, soybean seed weight showed significantly correlation (p < 0.05) with nitrogen-metabolism-related parameters. Based on the performance of growth, nitrogen metabolism, and yield attributes, CV.SN12 showed the highest tolerance to drought, followed by CV.SN8 and CV.SN17. In addition, these nitrogen-metabolism-related parameters could be used in soybeans to select for drought tolerance.