Wild soybean (Glycine soja), the ancestor of cultivated soybean, has evolved into many ecotypes with different adaptations to adversity under the action of divergent evolution. Barren-tolerant wild soybean has developed adaptation to most nutrient-stress environments, especially with respect to low nitrogen (LN) conditions. This study describes the differences in physiological and metabolomic changes between common wild soybean (GS1) and barren-tolerant wild soybean(GS2) under LN stress. Compared with plants grown under the unstressed control (CK) conditions, the young leaves of barren-tolerant wild soybean under LN conditions maintained relatively stable chlorophyll, concentration and rates of photosynthesis and transpiration, as well as increased carotenoid content, whereas the net photosynthetic rate (PN) of GS1 decreased significantly 0.64-fold (p< 0.05) in the young leaves of GS1. The ratio of internal to atmospheric CO2concentrations increased significantly 0.07-fold (p< 0.05), 0.09-fold (p< 0.05) in the young leaves of GS1 and GS2, respectively, and increased significantly 0.05-fold (p< 0.05) and 0.07-fold (p< 0.05) in the old leaves of GS1 and GS2, respectively, relative to the CK. The concentration of chlorophylls a andbdecreased significantly 0.45-fold (p< 0.05), 0.13-fold (p> 0.05) in the young leaves of GS1 and GS2, respectively, and decreased significantly 0.74-fold (p< 0.01) and 0.60-fold (p< 0.01) in the old leaves of GS1 and GS2, respectively. Under LN stress, nitrate concentration in the young leaves of GS1 and GS2 decreased significantly 0.69- and 0.50-fold (p< 0.01), respectively, relative to CK, and decreased significantly 2.10-fold and 1.77-fold (p< 0.01) in the old leaves of GS1 and GS2, respectively. Barren-tolerant wild soybean increased the concentration of beneficial ion pairs. Under LN stress, Zn2+significantly increased by 1.06- and 1.35-fold (p< 0.01) in the young and old leaves of GS2 (p< 0.01), but there was no significant change in GS1. The metabolism of amino acids and organic acids was high in GS2 young and old leaves, and the metabolites related to the TCA cycle were significantly increased. The 4-aminobutyric acid (GABA) concertation decreased significantly 0.70-fold (p< 0.05) in the young leaves of GS1 but increased 0.21-fold (p< 0.05) significantly in GS2. The relative concentration of proline increased significantly 1.21-fold (p< 0.01) and 2.85-fold (p< 0.01) in the young and old leaves of GS2. Under LN stress, GS2 could maintain photosynthesis rate and enhance the reabsorption of nitrate and magnesium in young leaves, compared to GS1. More importantly, GS2 exhibited increased amino acid and TCA cycle metabolism in young and old leaves. Adequate reabsorption of mineral and organic nutrients is an important strategy for barren-tolerant wild soybeans to survive under LN stress. Our research provides a new perspective on the exploitation and utilization of wild soybean resources.