Background: The lower reaches of the Tarim River is an arid region of inland China. In this area, vegetation is sparse and the environment is fragile. Therefore, it is of great significance to study the structure and stability of the plant community and ecosystem in the lower reaches of the Tarim River. It is valuable to increase the understanding of ecological protection and restoration in arid areas. Methods: In this study, four sections, Yingsu, Karday, Alakan, and Yiganbjm, were selected as research sites, and 96 arbor and shrub quadrats and 288 herb quadrats were delimited in these sites. The ecological characteristics of all species in the quadrats were investigated. We selected the surveyed data from 2000, 2004, 2008, 2012, 2016, and 2019. Based on the data, we analyzed the variations in species composition. We also determined Shannon-Wiener indexes, Alatalo indexes, and ecological dominance to discuss the species diversity and uniformity of plant community. Plant community stability were also evaluated. Results: There were 17 species in 2000 and 31 species in 2019. The proportion of arbor and shrub species decreased, while the understory herbaceous species gradually increased; all of the species become balanced. The stability of the plant community gradually increased; however, it remained unstable. Conclusions: In general, water conveyance in an ecosystem plays a positive role in promoting the restoration of vegetation and ecological stability. This study provides a new method for the evaluation of ecological protection and restoration benefits in arid areas. Our findings can be a good reference for similar studies.