Relationship between standing vegetation and soil seed bank in flooded area, non-flooded area and control area in water-level-fluctuating Zone of Three Gorges Reservoir at the beginning after charging water was studied with a germination method. The results showed that the standing vegetation was composed of 100 species in 71 genera of 47 families in flooded area, and 223 species in 163 genera of 84 families in non-flooded area, and, the main families were Asteraceae, Leguminosae, Poaceae, Rosaceae, Cyperaceae. The species life of the standing vegetation is mainly composed of annual herbaceous species which had a short growth cycle and strongly adaptability accounted for majority proportion. Shrub and fluorescence accounted for 19% in flooded area. In non-flooded area, annual herbaceous species, perennial herbage species, shrub, fluorescence and arbor accounted respectively for 20.45%,36.36%, 28.28%, 15%. The life form percentage in control area which existed the original vegetation were respectively 23.24%, 28.18%, 32.02%, 17.05%. Compared with those in control area, both species diversity indices and richness indices of the standing vegetation decreased significantly in flooded area, and however increased significantly in non-flooded area. Evenness indices were all decreased in both flooded and non-flooded area. The species number of the seed bank in flooded area and non-flooded area were respectively 79 and 108, with 9 and 38 species more than that in control area. There existed significant differences in the soil seed bank among flooded area, non-flooded area and control area, with an average seed density being (12667±222525) seed banks per m2, (38013±9796.04) seed banks per m2 and (18715±8234.77) seed banks per m2, respectively. Compared with control area, flooded area had lower seed bank density by 32.32% and non-flooded area had higher seed bank density by 103.12%. Herbaceous species accounted for majority proportion in these two sites, and annual herbaceous species seeds were higher proportion than that of the perennial herbaceous. The indices of biodiversity, richness, evenness of the seed bank had similar trends to the standing vegetation, with a smaller extent of the change. There were 9, 40, and 15, co-occurrence species in both the standing vegetation and the seed bank respectively in flooded area, non-flooded area and control area. Their Sorensen similarity coefficients of species composition between the seed bank and the standing vegetation were respectively 0.328, 0.241and 0.186. The results indicated similarity coefficients were lower in the water-level-fluctuating Zone of Three Gorges Reservoir at the beginning after charging water, and soil seed bank of dominant species that did not quickly form dominant communities in the standing vegetation. Which had a great relationship with the shorter formation time of water-level-fluctuating zone of Three Gorges Reservoir.