Trade-Off between Root Efficiency and Root Size Is Associated with Yield Performance of Soybean under Different Water and Phosphorus Levels

(1) Background: Root traits play important roles in acclimating to water and phosphorus (P) shortages. However, the relative importance of root size and efficiency under these conditions is unknown. (2) Methods: This study investigated the role of root size and efficiency in acclimating to water- and P-limited environments. Three soybean genotypes with contrasting root sizes were grown in tall cylindrical pots to compare grain yield, root density, and water- and nutrient-uptake efficiencies under two water (well-watered and water-stressed) and three P levels (0 (P0), 60 (P60), and 120 (P120) mg P kg−1 dry soil). (3) Results: Water or P deficit, and combined water and P deficit significantly decreased grain yield, which was associated with greater P uptake per unit root dry weight (DW) under water stress. The genotype Zhonghuang 30 (ZH) with the greatest water, nitrogen, and P uptakes per unit root DW had the highest grain yield at P60 and P120 under water stress and P0 under well-watered conditions, but ZH had the lowest grain yield at P60 and P120 under well-watered conditions, due to its small root size. (4) Conclusions: High root efficiency—which was correlated with high root density—improved grain yield under P- and water-limited conditions, but restricted yield potential when P and water were not limited.