Waterlogging has become one of the major abiotic stress to a variety of plants including maize in southern China. Investigating the biological characteristics of waterlogging tolerance, creating new waterlogging resistant maize germplasm and cultivating new waterlogging resistant maize varieties are the most economical and effective way to reduce the loss of maize yield. In this study, multiple evidences showed that maize BMY (Baimaya) was more waterlogging tolerant than maize B73. At the phenotypic level, SPAD (soil plant analysis development) value, root and shoot fresh weight, root and shoot dry weight, seedling height, number of adventitious roots and root length of BMY were significantly higher than those of B73 under waterlogging stress. After 28 days of waterlogging, the average survival rate of BMY was 86%, while B73 was only 8.25%, indicating that BMY, due to its better developed adventitious roots and the formation of aerenchyma induced under waterlogging stress, had a higher tolerance to waterlogging than B73 (P=2.45E-08). At the physiological and biochemical level, MDA (malondialdehyde) content in B73 increased significantly after 6 days of waterlogging, while it remained at a relatively low level in BMY. Moreover, POD (peroxidase) and SOD (superoxide dismutase) contents of BMY rapidly accumulated after waterlogging stress, in contrast to its relatively low level in B73, which proved that BMY had a strong scavenging ability of reactive oxygen species. The strong phosphorus absorption capacity of BMY enhanced its ability to resist abiotic stress. This study revealed the morphological and physiological basis of waterlogging tolerance at the seedling stage of the local germplasm BMY, and provided a theoretical basis for further use of this germplasm for breeding of waterlogging tolerant varieties.