Due to the operation of the Three Gorges Dam and upstream reservoir groups, the hydrological rhythm of the middle and lower reaches of the Yangtze River has changed subsequently, which resulted in habitat changes in Lake Dongting. However, these habitat changes not only affect the distribution of wetland vegetation but also influence the soil seed bank in Lake Dongting. To explore the influence of soil moisture variation on wetland soil seed bank germination and the relationship between soil seed bank and ground vegetation, 11 typical sites were set in field investigation, which were classified into 5 kinds of floodplains (silt floodplain, silt and grass transition zone, grass floodplain, grass and reed transition zone, reed floodplain). In addition, soil seed bank germination experiment was carried out under two types of treatment (moisture and flooded conditions). The results revealed that soil moisture decreased from silt floodplain to the reed floodplain. The density of soil seed bank of 5 floodplains had no significant difference. In the germination experiment, the species richness and soil seed bank density in moisture group was significantly higher than in the water flooded group, besides, the species richness and seed bank density in soil seed bank of East Dongting Lake Nature Reserve were significantly higher. Moreover, the species richness of ground vegetation was higher than soil seed bank, and the Jaccard similarity index of soil seed bank and surface vegetation in silt floodplain was the lowest. Phalaris arundinacea, Phragmites communis and Miscanthus sacchariflorus only existed in ground vegetation, while Lindernia procumbens and Mazus japonicus only existed in soil seed bank. In conclusion, it is not possible to rely solely on the seed bank transplantation technology to restore vegetation, the seasonal water level change and the specificity of some species should also be put into consideration. Meanwhile, matching targeted hydrological regulation mechanisms and related artificial measures can help to rehabilitate successfully.