[Objective] The objective of the study is to explain changes in natural vegetation communities after flooding and explore the impacts of different flooding modes on surface soil salinity and to provide the theoretical basis for vegetation restoration and reconstruction of artificial vegetation in lower reaches of Tarim river.[Methods] Based on the long-term field investigation, this paper measured the salt content of 399 surface soil samples collected from water flooding area and non-water flooding area with electric conductivity method, and discussed the effects of different flooding disturbances on salt content in surface soil.[Results] The total soil salt contents in the lower reaches of Tarim river were generally higher, which affected the distribution and growth of nature vegetation, but after flooding disturbance, the salinity of surface soil declined significantly. The results of ANOVA analysis about soil salinity of surface soil under different flooding modes showed that the effect of higher frequency on the total soil salt contents were more significant than lower frequency, but long-term submerge was disadvantageous for soil desalination, so the effect of flooding mode for soil salinity were significant.[Conclusion] The natural vegetation community varied after flooding for the decline of salinity in surface soil, and flooding disturbance with intermediate frequency and duration was beneficial for the ecology restoration in the lower reaches of the Tarim river.