In recent years, a number of high dams and reservoirs have been built in the southwestern basin of China, and the resulting large-area reservoir drawdown zone or water-level-fluctuating zone (WLFZ) is facing problems such as plant restoration. Scientific basis to draw lessons from the existing achievements and experiences of phytoremediation in the Three Gorges Reservoir (TGR) still lacks. Based on the investigation of the existing plants in the WLFZ of the TGR and the Southwest Reservoir during the emergence period in 2021, the WLFZ was divided according to the flooding time, severe flooded areas (S) with a flooding time of 7 months or more, moderate flooded areas (M) with a flooding time of 5 to 6 months, and light flooded areas (L) with a flooding time of 4 months or less. The species composition, species diversity and phylogenetic diversity of the WLFZ of the TGR and the Southwest Reservoir along each flooding gradient were quantitatively compared. The driving factors of species composition, plant community assembly strategy and diversity maintenance mechanism of the WLFZ of the reservoirs were discussed. The results showed that 36 species of vascular plants, belonging to 20 families and 36 genera, were found in the WLFZ of the TGR, and 45 vascular plant species belonging to 21 families and 41 genera recorded in the WLFZ of the Southwest Reservoir. The Jaccard and Sorensen similarity coefficients of species composition in the TGR and southwest areas were 30.65% and 46.91%, respectively, with annual as the main life form and Compositae and Gramineae as the dominant families. Similar flooding time may be the main factor leading to the similarity of species composition between the two regions. The Gleason richness index, Shannon-Wiener complexity index, Simpson dominance index and Pielou evenness index in the southwest study area were better than those in the TGR area. The species diversity of the two areas increased with flooding degree decrease. Species diversity may be maintained by a combination of environmental filtering, seed dispersal limitation, habitat heterogeneity and region species pool. The phylogeny level of community in the TGR and southwest study area was low, and negatively correlated with flooding time. The former increased more, and the phylogeny level of L section was significantly higher than the latter. In addition to the no obvious trend in the L section of the southwest study area, the vegetation phylogenetic structure of the TGR and the southwest study area is divergent at the overall level and in each flooding gradient section, mainly composed of distant species, and the community assembly is dominated by random processes.