To investigate the water-saving cultivation and water-efficiency use of soybean, we selected a soybean variety widely cultivated in Henan province, China — Glycine max ‘zheng92116’ — to determine the effect of short-term soil drought and rewatering during the blooming stage on soybean leaf photosynthesis and yield. As compared with leaf water content, stomatal conductance (Gs) was more sensitive to soil water deficiency . At 2 days after water was withheld, when the soil relative water content dropped to 27.2%, Gs and net photosynthetic rate (Pn) decreased to 54.1% and 81.1%, respectively, in experimental leaves, but the leaf water potential did not differ from control leaves. After rewatering, leaf water potential and Pn recovered quickly; transpiration rate (Tr), Gs and intercellular CO2 concentration (Ci) of the treatment group were significantly higher than those of the control group 3 days after rewatering, which showed a super-compensation effect. The drought treatment led to a significant decrease in leaf and stem biomass of soybean, which resulted in a 16.7% increase in ratio of root to shoot and a 26.3% increase in harvest index. The results suggested that short-term drought at the blooming stage could significantly influence soybean yield and biomass.