Abstract: Waterlogging is one of the most important stresses in soybean production. Studying the responses of soybean to waterlogging and understanding its mechanism of waterlogging tolerance are essential for improving the stress resistance of soybean varieties and formulating the agronomic strategies for waterlogging management in the field. In this review, we described the effects of waterlogging on soybean growth and development, yield components, physiological and biochemical processes including photosynthesis, respiration and contents of endogenous hormones, introduced the identification methods for waterlogging tolerance, analyzed the genetic patterns and molecular mechanisms of waterlogging tolerance in soybean, and summarized the progress in soybean variety development for waterlogging tolerance. Furthermore, we discussed the problems and trends of the waterlogging tolerance studies in soybean and crops.