The periodical fluctuation of water-level-fluctuating zone in Three Gorges Reservoir led to the variation of the soil ecological environment between wet and dry state. This variation inevitably produce a greater change in the soil seed bank, which further affects the standing vegetation recovery and growth. In this paper, we studied the dynamic variation of soil seed bank in water-level-fluctuating zone of Three Gorges Reservoir at the beginning after charging water was studied by substituting flooding time gradient with vertical space gradient. As soil seed bank density of clear-cutting land increased gradually with time, the density of abandoned farmland decreased. With the vertical space gradient increasing, density of soil seed bank in water-level-fluctuating zone in May, July, September showed gradual increasing trend respectively. The above results suggested that the longer flooding dures, the smaller soil seeds storage amount is. Co-occuring dominant species in different months, including Ficus tikoua, Youngla japonica, Cyperus microiria, Digitaria chrysoblephara, Veronica didyma, Mazus miquelii, Gnaphalium affine, Cardamine lyrata, Pouzolzia zeylanica, Veronicastrum stenostachyum, Cyperus rotundus, Erigeron annuus, Eragrostis ferruginea and Boehmeria nivea, were main components of soil seed bank. These species had a strong adaptability to the fluctuating environmental changes. The life-form composition of soil seed bank in different months was very similar. They were mainly composed of seeds of annual and perennial herbs, while being relatively lack of the seeds of shrub and arbor. Moreover, the life form composition proportions of soil seed banks of different altitude space were different. Combining with water ecological function of the soil seed bank, we can divided it into hygrophytes, hygromesophytes, mesophytes and mesoxerophytes. They were mainly mesophytes based, the proportion of mesoxerophytes in high-altitude section and that of hygromesophytes in low altitudes of were relatively high, while the proportion of hygrophytes in different altitude section in different months changes only a little. This indicated water flooded caused mesophytes and hygromesophytes gradually increasing in the soil seed bank, which was also the change trend of plant water ecological function type in water-level-fluctuating zone. The plants in soil seed bank had higher biological diversity as well as the plant species was high variable in different elevation sections and was lack of absolute dominant species. The vegetation communities were obviously in its early succession stage. In conclusion, from the results of the soil seed bank of water-level-fluctuating zone in Three Gorges Reservoir, vegetation restoration and reconstruction of the potential were unrealistic. This suggested that the changes of habitat, spesies composition and seed reserves of the soil seed bank were drastic at the beginning after charging water. In order to restore the vegetation of water-level-fluctuating zone more quickly, more manual intervention need to be introduced rather than only depending on the original ones.