An investigation was made on the standing vegetation and soil seed bank in desert riparian forest in lower reaches of Tarim River under effects of river-flooding. The results showed that the standing vegetation in non-flooded and flooded sites was composed of 14 species in 13 genera of 8 families, and 26 species in 21 genera of 10 families, respectively, and some shallow-rooted and hygrophilous species were recorded in flooded sites. The indices per unit area plant species number, vegetative coverage, plant density, and species diversity of the vegetation were all higher in flooded than in non-flooded sites. The species number of the soil seed bank in flooded sites was 19, with 5 species more than that in non-flooded sites, and the seed bank density in flooded sites was 2.94 times higher than that in non-flooded sites. The proportion of annual herbaceous species seeds in flooded sites increased by 23.07% while that of shrub species seeds decreased by 20.99%, compared with those in non-flooded sites, and the proportion of perennial herbaceous species seeds had less difference between these two sites. River-flooding increased the diversity of soil seed bank. In flooded and non-flooded sites, the co-occurrence species in seed bank and in standing vegetation were 18 and 9, with the similarity coefficients of species composition between soil seed bank and standing vegetation being 0.842 and 0.667, respectively.