Phosphorus (P) is an essential nutrient element for plants. Wild soybean (Glycine soja) expresses higher tolerance to P-limited environment compared to cultivated soybeans (Glycine max). In this study, the response of ionomics and metabonomics in young and old leaves of two soybean varieties under low P were studied. Our results showed that the tolerance of low P in wild soybean can be improved by promoting the accumulation of Mg2+, Fe3+, and SO42- in young and old leaves and the transportation of NO3− and H2PO4− from old to young leaves. The young and old leaves of wild soybean under low P accumulated sugars including maltose and sucrose, amino acids including asparagine and glutamine, and nitrogenous compounds including tyramine, and enhanced the tricarboxylic acid cycle metabolism, especially in young leaves, but decreased the content of hexose-phosphate metabolites. Our experiment indicated that wild soybean can tolerate low P by enhancing the energy metabolism in young and old leaves, promoting the transportation and reuse of sugars and amino acid metabolites from old to young leaves, and mobilizing Pi from hexose-phosphate of old leaves to young leaves. Our results provide a new insight for the cultivation of new soybean varieties with tolerance to P deficiency.