The invention discloses a method for evaluating flood tolerance of the maize variety. The method comprises the following steps of 1, after a pot is drowned, performing evaluation on four indexes, such as the color of a leaf, the form of the leaf, the color of a stem and the form of a root to preliminarily determine the flooding tolerance level; 2, performing two-sample pairing statistic analysis method on 15 shapes subjected to preliminary screening in the first step, and taking the strain height, the net photosynthetic rate, the green area, the root biomass, the root growth rate, the content of chlorophyll a, the total content of chlorophyll and an SPAD (soil and plant analyzer development) value as flood tolerance degree evaluation indexes according to the waterlogging influence degree; and 3, performing clustering analysis on the authentication indexes obtained by the second step, and classifying the varieties with different flood tolerance degrees into a flood tolerance hybrid and a non flood tolerance hybrid near to 27 according to genetic distances of all property clusters. The method for quickly and easily obtaining the flood tolerance evaluation indexes in a maize seedling stage is established according to the form change of leaves and stems above the ground as well as the physiologic and morphologic expression of plants, so that a basis is supplied to correct selection of the maize variety in an easily flooding region.