A major quantitative trait locus (qPE19) was identified in soybean that controls seven low-phosphate (LP) tolerance-related traits. The gene responsible for qPE19 was identified as GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2 (GmGDPD2), with haplotype 5 being 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 reduced traits. GmMyb73 negatively regulates GmGDPD2 by binding to its promoter, thus negatively regulating LP tolerance. GmGDPD2 physically interacts with GA2ox1, and overexpression of GmGA2ox1 enhances LP-related traits. Analysis of double mutants for GmGDPD2 and GmGA2ox1 showed that GmGDPD2 regulates LP tolerance by influencing auxin and gibberellin-related cell division in the root. These findings reveal a regulatory module (Myb73–GDPD2–GA2ox1) that plays a major role in regulating LP tolerance in soybeans and is expected to be used to develop phosphate-efficient soybean varieties to enhance soybean production, particularly in phosphate-deficient soils. The study highlights the importance of understanding the molecular mechanisms underlying phosphate absorption and utilization in soybean to develop strategies for improving P uptake and use efficiency in this important crop. The results suggest that the Myb73–GDPD2–GA2ox1 module could be used in marker-assisted breeding or genetic engineering strategies to design Pi-efficient soybean varieties.A major quantitative trait locus (qPE19) was identified in soybean that controls seven low-phosphate (LP) tolerance-related traits. The gene responsible for qPE19 was identified as GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE2 (GmGDPD2), with haplotype 5 being 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 reduced traits. GmMyb73 negatively regulates GmGDPD2 by binding to its promoter, thus negatively regulating LP tolerance. GmGDPD2 physically interacts with GA2ox1, and overexpression of GmGA2ox1 enhances LP-related traits. Analysis of double mutants for GmGDPD2 and GmGA2ox1 showed that GmGDPD2 regulates LP tolerance by influencing auxin and gibberellin-related cell division in the root. These findings reveal a regulatory module (Myb73–GDPD2–GA2ox1) that plays a major role in regulating LP tolerance in soybeans and is expected to be used to develop phosphate-efficient soybean varieties to enhance soybean production, particularly in phosphate-deficient soils. The study highlights the importance of understanding the molecular mechanisms underlying phosphate absorption and utilization in soybean to develop strategies for improving P uptake and use efficiency in this important crop. The results suggest that the Myb73–GDPD2–GA2ox1 module could be used in marker-assisted breeding or genetic engineering strategies to design Pi-efficient soybean varieties.