Salinity is one of the major environmental stresses impeding crop growth, which can lead to a series of morphological, physiological, biochemical and molecular changes that severely reduces agricultural yields and productivity. The ability to tolerate salinity stresses differs widely among species of plants as well as within different varieties in the same species. As an important cash crop, productivity of soybean can be significantly hampered by soil salt stresses and high salinity can sharply decline growth and give bad impacts on variable agronomy traits, seed quality and quantity, and finally reduce its commercial yield. Although most soybean varieties are sensitive to salt stresses, soybean germplasms display a spectrum of salt tolerance capability from high to low. Moreover, the degree of salt tolerance of soybean varieties varies among different developmental stages. To achieve a better understanding of salt tolerant mechanisms of soybean varieties, and determine the most reliable indicators for distinguishing high salt-tolerance varieties, seeds of 4 soybean varieties (respectively, 21066-2, 22021-1, 22293-1 and 22451-1 provided by Harbin Agricultural Academy of Science) were sowed in soil containers(45 cm in length,32 cm in width, 13.5 cm in height) for simulating natural growth conditions, and their salt tolerance capability in emergence and seedling stages under 150 mmol/L NaCl treatments were evaluated in this paper through measuring variable morphological and physiological parameters including plant height, hypocotyls length, lateral root numbers, fresh and dry weight of shoots and roots, contents of malondialdehyde (MDA) and free proline (Pro), activity of superoxide dismutase (SOD) in emergence and seedling stages. And then the seedlings were transplanted into field for recording seed yield at their natural maturity. Our results clearly showed that NaCl treatments could strongly decrease the plant height, fresh and dry weight of shoots and roots of the 4 varieties both in their emergence stage and seedling stage, while lateral root numbers and hypocotyls length decreased in the emergence stage but increased in the seedling stage. Under the unstressed control condition, MDA content and SOD activity in the salt-tolerant 22021-1 variety were significantly higher than those in the salt-sensitive 22293-1 variety both in the emergence stage and seedling stage (P<0.05). However, MDA content sharply decreased (P<0.01) and SOD activity significantly increased (P<0.05) in salt-tolerant 22021-1 variety after exposure to salt stresses, i.e, 51.03% and 21.45% declines in MDA content and 5.85% and 45.77% enhancements in SOD activity were respectively found in the emergence stage and seedling stage. Different from 22021-1, 22293-1 variety showed a 58.97% increase in the MDA content (P<0.01) in emergence stage but no significant change in seedling stage (P>0.05), while these salt stresses slightly increased the SOD activity in the two stages but cannot be up to statistical significance (P>0.05). The final commercial yield was affected by the short-term salt stress treatments, but differed in different soybean varieties. Generally, the salinity tolerance or sensitivity of soybean varieties were well related to their antioxidant response, and high salt stress tolerability in the 22021-1 variety was associated with the ability of maintaining higher SOD activity for lowering the possible lipid peroxidation. Our finding indicates that leaf MDA level and SOD activity could be used as two physiological indices for assessing the salt tolerability of variable soybean varieties.