Soybean domestication has significantly changed key agronomic traits, yet its impact on leaf photosynthetic phosphorus-use efficiency (PPUE) and its underlying traits remain poorly known. Further information on this would be important to increase soybean P-use efficiency. To address this gap, 48 soybean accessions (16 wild relatives, 16 landraces and 16 cultivars) were used to compare leaf anatomical traits, foliar chemical P fractions, P allocation and PPUE under two P levels. The results showed that the cultivars had higher area-based and mass-based photosynthesis rates, PPUE, metabolite P concentration, and its percentage of leaf total P, as well as a greater percentage of lipid P, nucleic acid P and residual P. Conversely, wild relatives tended to have higher leaf P concentration, palisade:spongy thickness ratio, and concentrations of inorganic P, nucleic acid P, lipid P and residual P. PPUE was negatively correlated with leaf inorganic P concentration and its percentage relative to leaf total P, while it was positively correlated with the concentration and percentage of metabolite P. We concluded that soybean domestication increased PPUE, as a result of both increased photosynthesis rate and decreased leaf P concentration; domestication reduced the palisade:spongy thickness ratio coupled with increased allocation of P to P-containing metabolites, thereby contributing to faster photosynthesis and higher PPUE. This study shed light on the significance of leaf P allocation and anatomical traits affecting PPUE during soybean domestication, offering a mechanistic understanding to further enhance soybean P-use efficiency.