Maize is extremely sensitive to waterlogging stress. A pot experiment was conducted to study the morpho-physiological characteristics of 18 differrent maize cultivars (widely grown in South China) under waterlogging stress at seedling stage. Results showed that maize shoot growth was inhibited in terms of plant height and dry weight whilst leaf chlorophyll contents were also decreased under waterlogging stress. Root length, root hairs, root surface area and root volume were also declined under waterlogged conditions. Furthermore, activity of antioxidants i.e., superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were increased considerably under waterlogging stress compared to control. The soluble protein content also increased in some maize cultivars whereas malondialdehyde (MDA) contents were found to be decreased in some cultivars that may be due to higher antioxidant enzyme activities. Furthermore, the principal component analysis (PCA) showed that the coefficients of comprehensive indices (Z) for protein contents, SOD, POD and CAT were higher in Z1, the soluble protein content and MDA content in Z2 while the SPAD and F v /F m values in Z3 were remained higher than other parameters.