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Drought stress is a common issue that affects agriculture production. The soybean plant is one of the drought-sensitive crops that could lose the yield of up to 40% under severe drought years. Improvements in drought tolerance have been one of the main objectives of breeding programs in soybean. In this study, 62 soybeans [
Glycine max
(L.) Merri.] germplasms including landraces and elite cultivars were evaluated by analyzing canopy and root morphological characteristics at seedling stage under polyethylene glycol (2.5 M PEG 8000, − 0.54 MPa) simulated drought stress. The results showed that the wilting index of sixty-two soybean germplasms showed significant polymorphism differences after 4 days PEG treatment. The lowest wilting index was 2.75 in Tiefeng 31, while the largest reached 9 in Fengdou 93 and Songzidou. The wilting index was positively correlated with plant height, electrolyte leakage, and negatively correlated with a dry weight of the above-ground part, stomatal conductance, and transpiration rate by regression analysis. The root system architecture (RSA) study showed root-canopy ratio, root length, number of the lateral roots, root surface area, and root volume were significantly negatively correlated with the wilting index and positively correlated with the root volume. Based on these results, sixty-two soybean germplasms were comprehensively evaluated for drought-tolerant cultivar by the principal component analysis (PCA). The results showed that Tiefeng 31 was the most drought-tolerant elite cultivar. However, Fengdou 93 was the most drought-sensitive elite variety. The drought tolerance screening results were consistent with the wilting index and RSA analysis, especially the root length. Both droughts tolerant and sensitive elite cultivar could be further used to breed drought-tolerant germplasms and to clarify the drought tolerance mechanism in soybean.