Drought and flooding stress alternately and frequently occur in Guangxi, China, and the whole world, which seriously limit maize production. Few studies focus on the different responses and evaluations of maize to drought and flooding stresses. A pot experiment with 40 varieties was conducted under well water, drought and flooding stresses. A multivariate analysis method of principal component analysis, comprehensive evaluation value, correlation analysis, stepwise regression analysis, and cluster analysis was used to evaluate the resistance of maize. Most varieties had stronger drought resistance rather than flooding resistance because of the higher antioxidant enzyme activities, osmotic adjustment substances, less reactive oxygen species, and a greater than 1.0 drought-resistance coefficient. However, there was an increment of reactive oxygen species (especially O2-), ascorbate peroxidase, peroxidase, soluble sugar, and the decrement of superoxide dismutase, catalase, soluble protein, and a lower than 1.0 of flooding-resistance coefficient of most maize varieties in flooding stress compared with well water. The superoxide dismutase, peroxidase, catalase, ascorbate peroxidase, proline, soluble sugar and protein, plant height, leaf area/plant, and stem diameter were screened out to be accurate and representative indicators to evaluate the drought and flooding resistance of maize. The study provides an insight to comprehend the different mechanisms of maize in response to drought and flooding stresses and provides a multivariate analysis method for screening the resistance of maize germplasm which could be valuable for further research and breeding of drought and flooding resistances of maize.