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In order to simplify the workload and find a reliable method for screening soybeans with different phosphorus (P) efficiencies, 47 soybean varieties were screened from 90 varieties according to yield under normal phosphorus, and 10 indicators including root phenotype, phosphorus utilization efficiency at the seedling stage and yield were measured. Through single-index cluster analysis, the performance value and relative value of the above-mentioned indexes under low-phosphorus conditions were analyzed, and then, the combined indexes were analyzed by principal components method. The membership function method and the cluster analysis method was used to calculate and analyze the comprehensive score value. Three indexes of root P utilization efficiency (X1), relative value of root P utilization efficiency (X2), and root volume (X3) under low P at the seedling stage were selected as the most consistent with the yield screening results under low P condition, and the mathematical model of the comprehensive score value was obtained:D=1.218X1+0.320X2+0.007X3-0.664 (P=0.000, R2=1.000). The comprehensive score can screen and identify the P efficiency of soybeans with fewer indexes in the early growth stages, which provides a more rapid and reliable mathematical model for screening and identifying a larger number of germplasm resources for P efficiency.