It's important to study the response of wetland plants to submergence and its recovery growth status for lacustrine wetland restoration. In this study, we revealed the varieties of relative chlorophyll content (rChlc), malondi-aldehyde content (MDA) and chlorophyll fluorescence characteristics of Phragmites communis in submergence every 5 d during one month in two types of sediment (one from Lake Chaohu (LS), and the other from farmland (AS)), and its recovery status in 10 d, 20 d and 30 d after submergence. Results showed that, compared to AS, P. communis growing in LS had higher rChlc and chlorophyll fluorescence characteristics during the rejuvenate period. rChlc decreased after submergence and obviously after 20 d, and further decreased by 40.82% and 39.49% in 30 d in LS and AS, respectively. However, MDA increased, and it was higher in AS than in LS. Chlorophyll fluorescence parameters Fv/Fm and Y both decreased, with significant correlation with rChlc varieties as a whole. The rapid light curves (RLCs) of P. communis growing in LS decreased slowly in 25 d, comparing to an obvious decrease in 15 d in AS. After submergence, rChlc and chlorophyll fluorescence characteristics of P. communis in two sediments all increased, with a greater range of the plant in AS than that in LS; however, they were both higher in LS than those in AS, and MDA had a same decreasing trend. It took longer time for P. communis to recover to the normal growth status with the extension of submergence, the leaves withered after 30 d submergence and sprouted new leaves and plant. At the same time, the recovery time was shorter of the plant grown in LS than that in AS. Consequently, submergence inhibits the growth of P. communis, and the inhibited effect is greater with the extension of submergence. It takes a short time for plant to recover to the normal growth status when in short submergence, and it needs to sprout new leaves and plants to adapt when in long submergence. Simultaneously, it's meaningful for P. communis to increase its submergence tolerance and recover growth after submergence when growing in sediment with relative better nutritional status.