The study identified a major quantitative trait locus (*qPE19*) controlling seven low-phosphate (LP)-related traits in soybean (*Glycine max*) through linkage mapping and genome-wide association studies (GWAS). The gene responsible for *qPE19* was identified as *GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2* (*GmGDPD2*), with haplotype 5 representing the optimal allele for LP tolerance. Overexpression of *GmGDPD2* significantly improved root architecture, phosphate efficiency, and yield-related traits, while CRISPR/Cas9-edited plants showed decreased performance. *GmMyb73* negatively regulates *GmGDPD2* by directly binding to its promoter, and *GmGDPD2* physically interacts with gibberellin 2-oxidase 1 (*GmGA2ox1*) in the plasma membrane. Overexpression of *GmGA2ox1* enhanced LP-associated traits similar to *GmGDPD2*. Double mutants for *GmGDPD2* and *GmGA2ox1* demonstrated that *GmGDPD2* regulates LP tolerance by influencing auxin and gibberellin dose-associated cell division in the root. These findings reveal a regulatory module, the Myb73–GDPD2–GA2ox1, that plays a major role in regulating LP tolerance in soybeans and has potential for developing phosphate-efficient varieties to enhance soybean production, particularly in phosphate-deficient soils.The study identified a major quantitative trait locus (*qPE19*) controlling seven low-phosphate (LP)-related traits in soybean (*Glycine max*) through linkage mapping and genome-wide association studies (GWAS). The gene responsible for *qPE19* was identified as *GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2* (*GmGDPD2*), with haplotype 5 representing the optimal allele for LP tolerance. Overexpression of *GmGDPD2* significantly improved root architecture, phosphate efficiency, and yield-related traits, while CRISPR/Cas9-edited plants showed decreased performance. *GmMyb73* negatively regulates *GmGDPD2* by directly binding to its promoter, and *GmGDPD2* physically interacts with gibberellin 2-oxidase 1 (*GmGA2ox1*) in the plasma membrane. Overexpression of *GmGA2ox1* enhanced LP-associated traits similar to *GmGDPD2*. Double mutants for *GmGDPD2* and *GmGA2ox1* demonstrated that *GmGDPD2* regulates LP tolerance by influencing auxin and gibberellin dose-associated cell division in the root. These findings reveal a regulatory module, the Myb73–GDPD2–GA2ox1, that plays a major role in regulating LP tolerance in soybeans and has potential for developing phosphate-efficient varieties to enhance soybean production, particularly in phosphate-deficient soils.