Zizania latifolia is a common emergent macrophyte in the middle and lower reaches of the Yangtze River Basin. In order to understand the expansion and degradation mechanism of Z. latifolia in the field, the morphological responses of Z. latifolia seedlings at different ages to short-term submergence are analyzed by simulation experiments. Two groups of seedlings with respective plant height of 36 and 70 cm were selected in this study. Three submergence treatments (0%, 50%, and 100% submergence) are tested in each group. The results showed that the morphological responses of aboveground part of the two groups of seedlings have certain differences. In treatment of 100% submergence, plant height was the lowest, and the shoot thickness and maximum leaf width were significantly lower than the other two treatments in 36 cm group. However, the plant height was the lowest in 0% submergence treatment, and no significant difference was detected between 50% and 100% submergence treatments in 70 cm group. Moreover, the morphological responses of root in the two groups also showed differences. All the six root parameters showed significant differences between 100% submergence treatment and the other two treatments in 36 cm group, while in the 70 cm group significant differences were found between 0% submergence treatment and the other two treatments. The total biomass and root/shoot ratio of the two groups of seedlings decreased with the increase of submergence depth. However, the two parameters were significantly lower in 100% submergence treatment than the other two treatments in 36 cm group, while no significant difference was found between 50% and 100% submergence treatments in 70 cm group. In conclusion, the morphological responses of Z. latifolia to short-term submergence were increased with the growth of the seedlings, and this had significant implications to the ecological regulation of Z. latifolia in lakes along the middle and lower reaches of the Yangtze River.