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Phosphorus (P) is essential for the growth and development of plants, playing crucial roles in energy acquisition, storage and utilization, regulation of enzyme activities, and yield formation. Therefore, P deficiency in soil is a main factor restricting crop production. The main reason is that crop yields depend on photosynthesis which is vulnerable to low P stress. Thus, it is important to study the relationship between photosynthesis and P efficiency. In this study, we evaluated the P efficiency by using the photosynthesis-related traits in 219 diverse soybean accessions across three different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). In total, 30 significant SNPs distributed in 14 genomic regions were identified to be associated with three photosynthesis-related traits under different P levels. Among the 14 associated regions, two regions (qP13 and qP19) were both found in two environments and explained 14.01% and 16.75% of the phenotypic variation, respectively. Furthermore, seven candidate genes underlying qP13 and qP19 were considered promising candidates involved in both soybean photosynthetic and low P tolerance. In all, we uncover two novel environmentally stable major genomic regions of P efficiency by using photosynthesis-related traits, which may provide more information for marker-assisted breeding in soybean and laying the foundation for simultaneously improving P efficiency and photosynthetic capacity. [ABSTRACT FROM AUTHOR]